Start testing: Feb 22 23:19 EST ---------------------------------------------------------- 1/90 Testing: GmxapiExternalInterfaceTests 1/90 Test: GmxapiExternalInterfaceTests Command: "${WORKDIR}/gromacs-2022/build/bin/gmxapi-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxapiExternalInterfaceTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests "GmxapiExternalInterfaceTests" start time: Feb 22 23:19 EST Output: ---------------------------------------------------------- [==========] Running 9 tests from 1 test suite. [----------] Global test environment set-up. [----------] 9 tests from GmxApiTest [ RUN ] GmxApiTest.ApiRunnerRestrainedMD Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 2 steps, 0.0 ps. Setting the LD random seed to -537153796 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.608 1.304 199.9 (ns/day) (hour/ns) Performance: 0.388 61.836 [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1613 ms) [ RUN ] GmxApiTest.RunnerBasicMD Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 2 steps, 0.0 ps. Setting the LD random seed to -576280577 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.973 1.487 200.0 (ns/day) (hour/ns) Performance: 0.340 70.490 [ OK ] GmxApiTest.RunnerBasicMD (1833 ms) [ RUN ] GmxApiTest.RunnerReinitialize Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 20 steps, 0.0 ps. Received the remote INT/TERM signal, stopping within 50 steps Setting the LD random seed to 2143277047 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 7.223 3.612 200.0 (ns/day) (hour/ns) Performance: 0.981 24.461 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 9.953 4.977 200.0 (ns/day) (hour/ns) Performance: 0.712 33.707 [ OK ] GmxApiTest.RunnerReinitialize (9022 ms) [ RUN ] GmxApiTest.RunnerChainedMD Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 2 steps, 0.0 ps. Setting the LD random seed to -1615401089 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.354 1.678 200.0 (ns/day) (hour/ns) Performance: 0.302 79.528 trr version: GMX_trn_file (single precision) Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.00390625 ps Run end step 2 Run end time 0.00390625 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.0078125 ps Run end step 4 Run end time 0.0078125 ps Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5.955 2.978 200.0 (ns/day) (hour/ns) Performance: 0.170 141.173 [ OK ] GmxApiTest.RunnerChainedMD (5016 ms) [ RUN ] GmxApiTest.Status [ OK ] GmxApiTest.Status (1 ms) [ RUN ] GmxApiTest.ApiRunnerStopSignalClient Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 1.041 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 4 steps, 0.0 ps. Setting the LD random seed to -587292945 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 7.879 3.945 199.7 (ns/day) (hour/ns) Performance: 0.214 112.206 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps Changing nstlist from 10 to 1, rlist from 1.041 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Water and methane' 4 steps, 0.0 ps. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.901 0.451 199.9 (ns/day) (hour/ns) Performance: 0.749 32.054 [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4869 ms) [ RUN ] GmxApiTest.SystemConstruction Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Setting the LD random seed to -6324250 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GmxApiTest.SystemConstruction (126 ms) [ RUN ] GmxApiTest.SaneVersionComparisons [ OK ] GmxApiTest.SaneVersionComparisons (1 ms) [ RUN ] GmxApiTest.VersionNamed0_1_Features [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) [----------] 9 tests from GmxApiTest (22485 ms total) [----------] Global test environment tear-down [==========] 9 tests from 1 test suite ran. (22529 ms total) [ PASSED ] 9 tests. Test time = 23.23 sec ---------------------------------------------------------- Test Passed. "GmxapiExternalInterfaceTests" end time: Feb 22 23:20 EST "GmxapiExternalInterfaceTests" time elapsed: 00:00:23 ---------------------------------------------------------- 2/90 Testing: GmxapiMpiTests 2/90 Test: GmxapiMpiTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxapiMpiTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests "GmxapiMpiTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 13 tests from 1 test suite. [----------] Global test environment set-up. [----------] 13 tests from GmxApiTest [ RUN ] GmxApiTest.AllContext [ OK ] GmxApiTest.AllContext (59 ms) [ RUN ] GmxApiTest.NullContext [ OK ] GmxApiTest.NullContext (1 ms) [ RUN ] GmxApiTest.MpiWorldContext [ OK ] GmxApiTest.MpiWorldContext (54 ms) [ RUN ] GmxApiTest.MpiSplitContext [ OK ] GmxApiTest.MpiSplitContext (49 ms) [ RUN ] GmxApiTest.ApiRunnerRestrainedMD Setting the LD random seed to -1085293105 Setting the LD random seed to 1072357214 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 18.00 Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 2 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 21.012 5.253 400.0 (ns/day) (hour/ns) Performance: 0.096 249.047 [ OK ] GmxApiTest.ApiRunnerRestrainedMD (5446 ms) [ RUN ] GmxApiTest.RunnerBasicMD Setting the LD random seed to -1140990209 Setting the LD random seed to -313524582 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 2 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.251 0.063 398.1 (ns/day) (hour/ns) Performance: 8.025 2.991 [ OK ] GmxApiTest.RunnerBasicMD (318 ms) [ RUN ] GmxApiTest.RunnerReinitialize Setting the LD random seed to -1692774423 Setting the LD random seed to 1600120751 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 20 steps, 0.0 ps. Received the remote INT/TERM signal, stopping within 50 steps Received the remote INT/TERM signal, stopping within 50 steps Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.307 0.077 398.6 (ns/day) (hour/ns) Performance: 46.005 0.522 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 20 steps, 0.0 ps. Writing final coordinates. NOTE: 44 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.089 0.022 395.1 (ns/day) (hour/ns) Performance: 157.929 0.152 [ OK ] GmxApiTest.RunnerReinitialize (296 ms) [ RUN ] GmxApiTest.RunnerChainedMD Setting the LD random seed to -142622850 Setting the LD random seed to -136383286 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 2 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.863 0.216 399.5 (ns/day) (hour/ns) Performance: 2.343 10.243 trr version: GMX_trn_file (single precision) trr version: GMX_trn_file (single precision) Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.00390625 ps Run end step 2 Run end time 0.00390625 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.0078125 ps Setting nsteps to 4 Run end step 4 Run end time 0.0078125 ps Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.00390625 ps Run end step 2 Run end time 0.00390625 ps Setting nsteps to 4 Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.0078125 ps Run end step 4 Run end time 0.0078125 ps Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.145 0.037 397.0 (ns/day) (hour/ns) Performance: 13.814 1.737 [ OK ] GmxApiTest.RunnerChainedMD (447 ms) [ RUN ] GmxApiTest.Status [ OK ] GmxApiTest.Status (1 ms) [ RUN ] GmxApiTest.ApiRunnerStopSignalClient Setting the LD random seed to -1294510 Setting the LD random seed to 1375526639 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 1.041 to 1 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 4 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.5%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.505 0.127 399.1 (ns/day) (hour/ns) Performance: 6.665 3.601 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps Changing nstlist from 10 to 1, rlist from 1.041 to 1 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Water and methane' 4 steps, 0.0 ps. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.9%. The balanceable part of the MD step is 26%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.212 0.053 397.7 (ns/day) (hour/ns) Performance: 6.342 3.784 [ OK ] GmxApiTest.ApiRunnerStopSignalClient (423 ms) [ RUN ] GmxApiTest.SystemConstruction Setting the LD random seed to -1141113093 Setting the LD random seed to -167909387 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data [ OK ] GmxApiTest.SystemConstruction (141 ms) [ RUN ] GmxApiTest.SaneVersionComparisons [ OK ] GmxApiTest.SaneVersionComparisons (1 ms) [ RUN ] GmxApiTest.VersionNamed0_1_Features [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) [----------] 13 tests from GmxApiTest (7242 ms total) [----------] Global test environment tear-down [==========] 13 tests from 1 test suite ran. (7296 ms total) [ PASSED ] 13 tests. Test time = 8.07 sec ---------------------------------------------------------- Test Passed. "GmxapiMpiTests" end time: Feb 22 23:20 EST "GmxapiMpiTests" time elapsed: 00:00:08 ---------------------------------------------------------- 3/90 Testing: GmxapiInternalInterfaceTests 3/90 Test: GmxapiInternalInterfaceTests Command: "${WORKDIR}/gromacs-2022/build/bin/workflow-details-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxapiInternalInterfaceTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests "GmxapiInternalInterfaceTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 2 tests from 1 test suite. [----------] Global test environment set-up. [----------] 2 tests from GmxApiTest [ RUN ] GmxApiTest.BuildApiWorkflowImpl Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Setting the LD random seed to -67142729 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GmxApiTest.BuildApiWorkflowImpl (130 ms) [ RUN ] GmxApiTest.CreateApiWorkflow Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Setting the LD random seed to 1861019507 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GmxApiTest.CreateApiWorkflow (120 ms) [----------] 2 tests from GmxApiTest (250 ms total) [----------] Global test environment tear-down [==========] 2 tests from 1 test suite ran. (294 ms total) [ PASSED ] 2 tests. Test time = 0.99 sec ---------------------------------------------------------- Test Passed. "GmxapiInternalInterfaceTests" end time: Feb 22 23:20 EST "GmxapiInternalInterfaceTests" time elapsed: 00:00:00 ---------------------------------------------------------- 4/90 Testing: GmxapiInternalsMpiTests 4/90 Test: GmxapiInternalsMpiTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxapiInternalsMpiTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests "GmxapiInternalsMpiTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 2 tests from 1 test suite. [----------] Global test environment set-up. [----------] 2 tests from GmxApiTest [ RUN ] GmxApiTest.BuildApiWorkflowImpl Setting the LD random seed to -274940426 Setting the LD random seed to -1075089438 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes [ OK ] GmxApiTest.BuildApiWorkflowImpl (130 ms) [ RUN ] GmxApiTest.CreateApiWorkflow Setting the LD random seed to -35193986 Setting the LD random seed to -1344345395 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data NOTE 1 [file spc_and_methane.top, line 33]: The bond in molecule-type methane between atoms 1 C and 2 H1 has an estimated oscillational period of 1.1e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group System is 18.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data [ OK ] GmxApiTest.CreateApiWorkflow (123 ms) [----------] 2 tests from GmxApiTest (254 ms total) [----------] Global test environment tear-down [==========] 2 tests from 1 test suite ran. (310 ms total) [ PASSED ] 2 tests. Test time = 1.07 sec ---------------------------------------------------------- Test Passed. "GmxapiInternalsMpiTests" end time: Feb 22 23:20 EST "GmxapiInternalsMpiTests" time elapsed: 00:00:01 ---------------------------------------------------------- 5/90 Testing: NbLibListedForcesTests 5/90 Test: NbLibListedForcesTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-listed-forces-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibListedForcesTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/listed_forces/tests "NbLibListedForcesTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 44 tests from 22 test suites. [----------] Global test environment set-up. [----------] 8 tests from NBlibTest [ RUN ] NBlibTest.BondTypesOperatorEqualWorks [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) [ RUN ] NBlibTest.BondTypesLessThanWorks [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) [ RUN ] NBlibTest.CanSplitListedWork [ OK ] NBlibTest.CanSplitListedWork (0 ms) [ RUN ] NBlibTest.ListedForceBuffer [ OK ] NBlibTest.ListedForceBuffer (0 ms) [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) [ RUN ] NBlibTest.GmxToNblibConversionAllTypes [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) [ RUN ] NBlibTest.EndToEndListedComparison [ OK ] NBlibTest.EndToEndListedComparison (0 ms) [ RUN ] NBlibTest.shiftForcesAreCorrect [ OK ] NBlibTest.shiftForcesAreCorrect (11 ms) [----------] 8 tests from NBlibTest (11 ms total) [----------] 1 test from Kernels [ RUN ] Kernels.HarmonicScalarKernelCanCompute [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) [----------] 1 test from Kernels (0 ms total) [----------] 1 test from FourCenter [ RUN ] FourCenter.ListedForcesProperDihedralTest [ OK ] FourCenter.ListedForcesProperDihedralTest (11 ms) [----------] 1 test from FourCenter (11 ms total) [----------] 7 tests from ThreeCenter [ RUN ] ThreeCenter.ListedForcesG96AngleTest [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) [ RUN ] ThreeCenter.ListedForcesLinearAngleTest [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) [----------] 7 tests from ThreeCenter (4 ms total) [----------] 5 tests from TwoCenter [ RUN ] TwoCenter.ListedForcesHarmonicBondTest [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) [ RUN ] TwoCenter.ListedForcesG96BondTest [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) [ RUN ] TwoCenter.ListedForcesCubicBondTest [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) [ RUN ] TwoCenter.ListedForcesMorseBondTest [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) [ RUN ] TwoCenter.ListedForcesFeneBondTest [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) [----------] 5 tests from TwoCenter (2 ms total) [----------] 5 tests from ListedExampleData [ RUN ] ListedExampleData.ComputeHarmonicBondForces [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) [ RUN ] ListedExampleData.ComputeHarmonicAngleForces [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) [ RUN ] ListedExampleData.CanReduceForces [ OK ] ListedExampleData.CanReduceForces (0 ms) [ RUN ] ListedExampleData.CanReduceEnergies [ OK ] ListedExampleData.CanReduceEnergies (0 ms) [----------] 5 tests from ListedExampleData (2 ms total) [----------] 1 test from LinearChainDataFixture [ RUN ] LinearChainDataFixture.Multithreading [ OK ] LinearChainDataFixture.Multithreading (122 ms) [----------] 1 test from LinearChainDataFixture (122 ms total) [----------] 2 tests from ListedShims [ RUN ] ListedShims.ParameterConversion [ OK ] ListedShims.ParameterConversion (0 ms) [ RUN ] ListedShims.GmxToNblibConversion [ OK ] ListedShims.GmxToNblibConversion (0 ms) [----------] 2 tests from ListedShims (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) [----------] 1 test from ListedTransformations [ RUN ] ListedTransformations.SortInteractionIndices [ OK ] ListedTransformations.SortInteractionIndices (0 ms) [----------] 1 test from ListedTransformations (0 ms total) [----------] Global test environment tear-down [==========] 44 tests from 22 test suites ran. (155 ms total) [ PASSED ] 44 tests. Test time = 0.83 sec ---------------------------------------------------------- Test Passed. "NbLibListedForcesTests" end time: Feb 22 23:20 EST "NbLibListedForcesTests" time elapsed: 00:00:00 ---------------------------------------------------------- 6/90 Testing: NbLibSamplesTestArgon 6/90 Test: NbLibSamplesTestArgon Command: "${WORKDIR}/gromacs-2022/build/bin/argon-forces-integration" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/samples "NbLibSamplesTestArgon" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 final position of particle 0: x 0.789162 y 1.271508 z 0.819867 Test time = 0.12 sec ---------------------------------------------------------- Test Passed. "NbLibSamplesTestArgon" end time: Feb 22 23:20 EST "NbLibSamplesTestArgon" time elapsed: 00:00:00 ---------------------------------------------------------- 7/90 Testing: NbLibSamplesTestMethaneWater 7/90 Test: NbLibSamplesTestMethaneWater Command: "${WORKDIR}/gromacs-2022/build/bin/methane-water-integration" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/samples "NbLibSamplesTestMethaneWater" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 final position of particle 9: x 77.358398 y 5.324894 z -80.600098 Test time = 0.12 sec ---------------------------------------------------------- Test Passed. "NbLibSamplesTestMethaneWater" end time: Feb 22 23:20 EST "NbLibSamplesTestMethaneWater" time elapsed: 00:00:00 ---------------------------------------------------------- 8/90 Testing: NbLibUtilTests 8/90 Test: NbLibUtilTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-util-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibUtilTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/util/tests "NbLibUtilTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 16 tests from 2 test suites. [----------] Global test environment set-up. [----------] 6 tests from NBlibTest [ RUN ] NBlibTest.isRealValued [ OK ] NBlibTest.isRealValued (0 ms) [ RUN ] NBlibTest.checkNumericValuesHasNan [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) [ RUN ] NBlibTest.checkNumericValuesHasInf [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect Velocities were taken from a Maxwell distribution at 300 K [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) [ RUN ] NBlibTest.generateVelocitySize Velocities were taken from a Maxwell distribution at 300 K [ OK ] NBlibTest.generateVelocitySize (0 ms) [ RUN ] NBlibTest.generateVelocityCheckNumbers Velocities were taken from a Maxwell distribution at 300 K [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) [----------] 6 tests from NBlibTest (1 ms total) [----------] 10 tests from NblibTraitsUtils [ RUN ] NblibTraitsUtils.FuseTwo [ OK ] NblibTraitsUtils.FuseTwo (0 ms) [ RUN ] NblibTraitsUtils.Fuse [ OK ] NblibTraitsUtils.Fuse (0 ms) [ RUN ] NblibTraitsUtils.Repeat [ OK ] NblibTraitsUtils.Repeat (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTuple1 [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTuple2 [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTypeList1 [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTypeList2 [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) [ RUN ] NblibTraitsUtils.Contains [ OK ] NblibTraitsUtils.Contains (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) [----------] 10 tests from NblibTraitsUtils (0 ms total) [----------] Global test environment tear-down [==========] 16 tests from 2 test suites ran. (1 ms total) [ PASSED ] 16 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "NbLibUtilTests" end time: Feb 22 23:20 EST "NbLibUtilTests" time elapsed: 00:00:00 ---------------------------------------------------------- 9/90 Testing: NbLibSetupTests 9/90 Test: NbLibSetupTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-setup-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibSetupTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/tests "NbLibSetupTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 56 tests from 3 test suites. [----------] Global test environment set-up. [----------] 41 tests from NBlibTest [ RUN ] NBlibTest.CubicBoxCannotHaveNaN [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) [ RUN ] NBlibTest.CubicBoxCannotHaveInf [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) [ RUN ] NBlibTest.RectangularBoxCannotHaveInf [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) [ RUN ] NBlibTest.CubicBoxWorks [ OK ] NBlibTest.CubicBoxWorks (0 ms) [ RUN ] NBlibTest.BoxEqual [ OK ] NBlibTest.BoxEqual (0 ms) [ RUN ] NBlibTest.NonBondedForceParamsCorrect [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) [ RUN ] NBlibTest.CanMergeInteractions [ OK ] NBlibTest.CanMergeInteractions (0 ms) [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) [ RUN ] NBlibTest.PbcHolderWorks [ OK ] NBlibTest.PbcHolderWorks (0 ms) [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) [ RUN ] NBlibTest.CanGetNumParticlesInMolecule [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) [ RUN ] NBlibTest.CanConstructExclusionListFromNames [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) [ RUN ] NBlibTest.AtWorks [ OK ] NBlibTest.AtWorks (0 ms) [ RUN ] NBlibTest.AtThrows [ OK ] NBlibTest.AtThrows (0 ms) [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) [ RUN ] NBlibTest.CanAddInteractions [ OK ] NBlibTest.CanAddInteractions (0 ms) [ RUN ] NBlibTest.CanAddUreyBradley [ OK ] NBlibTest.CanAddUreyBradley (0 ms) [ RUN ] NBlibTest.TopologyHasNumParticles [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) [ RUN ] NBlibTest.TopologyHasCharges [ OK ] NBlibTest.TopologyHasCharges (0 ms) [ RUN ] NBlibTest.TopologyHasMasses [ OK ] NBlibTest.TopologyHasMasses (0 ms) [ RUN ] NBlibTest.TopologyHasParticleTypes [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) [ RUN ] NBlibTest.TopologyHasParticleTypeIds [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) [ RUN ] NBlibTest.TopologyHasExclusions [ OK ] NBlibTest.TopologyHasExclusions (0 ms) [ RUN ] NBlibTest.TopologyHasSequencing [ OK ] NBlibTest.TopologyHasSequencing (0 ms) [ RUN ] NBlibTest.TopologyCanAggregateBonds [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) [ RUN ] NBlibTest.TopologyCanSequencePairIDs [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) [ RUN ] NBlibTest.TopologySequenceIdThrows No particle O-Atom in residue SOL in molecule SOL found [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) [ RUN ] NBlibTest.TopologyListedInteractions [ OK ] NBlibTest.TopologyListedInteractions (0 ms) [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows No particle Iron in residue SOL in molecule SOL found [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) [ RUN ] NBlibTest.toGmxExclusionBlockWorks [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) [----------] 41 tests from NBlibTest (1 ms total) [----------] 14 tests from NbnxmSetupTest [ RUN ] NbnxmSetupTest.findNumEnergyGroups [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) [ RUN ] NbnxmSetupTest.ewaldCoeffWorks [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) [ RUN ] NbnxmSetupTest.updateForcerecWorks [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) [ RUN ] NbnxmSetupTest.canCheckKernelSetup [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) [----------] 14 tests from NbnxmSetupTest (0 ms total) [----------] 1 test from VirialsTest [ RUN ] VirialsTest.computeVirialTensorWorks [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) [----------] 1 test from VirialsTest (0 ms total) [----------] Global test environment tear-down [==========] 56 tests from 3 test suites ran. (2 ms total) [ PASSED ] 56 tests. Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "NbLibSetupTests" end time: Feb 22 23:20 EST "NbLibSetupTests" time elapsed: 00:00:00 ---------------------------------------------------------- 10/90 Testing: NbLibTprTests 10/90 Test: NbLibTprTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-tpr-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibTprTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/tests "NbLibTprTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 4 tests from 1 test suite. [----------] Global test environment set-up. [----------] 4 tests from TprReaderTest [ RUN ] TprReaderTest.SimDBTprIsCreated NOTE 1 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2022 (single precision) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] TprReaderTest.SimDBTprIsCreated (3263 ms) [ RUN ] TprReaderTest.Spc2Reads NOTE 1 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2022 (single precision) Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] TprReaderTest.Spc2Reads (2889 ms) [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect NOTE 1 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2022 (single precision) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (2574 ms) [ RUN ] TprReaderTest.FCfromTprDataWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2022 (single precision) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] TprReaderTest.FCfromTprDataWorks (2586 ms) [----------] 4 tests from TprReaderTest (11313 ms total) [----------] Global test environment tear-down [==========] 4 tests from 1 test suite ran. (11357 ms total) [ PASSED ] 4 tests. Test time = 12.03 sec ---------------------------------------------------------- Test Passed. "NbLibTprTests" end time: Feb 22 23:20 EST "NbLibTprTests" time elapsed: 00:00:12 ---------------------------------------------------------- 11/90 Testing: NbLibIntegrationTests 11/90 Test: NbLibIntegrationTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-integration-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibIntegrationTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/tests "NbLibIntegrationTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 20 tests from 1 test suite. [----------] Global test environment set-up. [----------] 20 tests from NBlibTest [ RUN ] NBlibTest.GmxForceCalculatorCanCompute [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) [ RUN ] NBlibTest.ArgonVirialsAreCorrect [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) [ RUN ] NBlibTest.ArgonEnergiesAreCorrect [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms) [ RUN ] NBlibTest.ExpectedNumberOfForces [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) [ RUN ] NBlibTest.CanIntegrateSystem [ OK ] NBlibTest.CanIntegrateSystem (0 ms) [ RUN ] NBlibTest.UpdateChangesForces [ OK ] NBlibTest.UpdateChangesForces (0 ms) [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) [ RUN ] NBlibTest.CanConstructSimulationState [ OK ] NBlibTest.CanConstructSimulationState (0 ms) [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) [ RUN ] NBlibTest.SimulationStateCanMove [ OK ] NBlibTest.SimulationStateCanMove (0 ms) [ RUN ] NBlibTest.SimulationStateCanAssign [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) [ RUN ] NBlibTest.SimulationStateHasBox [ OK ] NBlibTest.SimulationStateHasBox (0 ms) [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) [----------] 20 tests from NBlibTest (7 ms total) [----------] Global test environment tear-down [==========] 20 tests from 1 test suite ran. (7 ms total) [ PASSED ] 20 tests. Test time = 0.69 sec ---------------------------------------------------------- Test Passed. "NbLibIntegrationTests" end time: Feb 22 23:20 EST "NbLibIntegrationTests" time elapsed: 00:00:00 ---------------------------------------------------------- 12/90 Testing: NbLibIntegratorTests 12/90 Test: NbLibIntegratorTests Command: "${WORKDIR}/gromacs-2022/build/bin/nblib-integrator-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbLibIntegratorTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/api/nblib/tests "NbLibIntegratorTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from NBlibTest [ RUN ] NBlibTest.IntegratorWorks [ OK ] NBlibTest.IntegratorWorks (0 ms) [----------] 1 test from NBlibTest (0 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (0 ms total) [ PASSED ] 1 test. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "NbLibIntegratorTests" end time: Feb 22 23:20 EST "NbLibIntegratorTests" time elapsed: 00:00:00 ---------------------------------------------------------- 13/90 Testing: TestUtilsUnitTests 13/90 Test: TestUtilsUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/testutils-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TestUtilsUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/testutils/tests "TestUtilsUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 59 tests from 5 test suites. [----------] Global test environment set-up. [----------] 10 tests from InteractiveTestHelperTest [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms) [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsMissingInput [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) [ RUN ] InteractiveTestHelperTest.DetectsExtraInput [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) [----------] 10 tests from InteractiveTestHelperTest (14 ms total) [----------] 34 tests from ReferenceDataTest [ RUN ] ReferenceDataTest.HandlesSimpleData [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) [ RUN ] ReferenceDataTest.HandlesFloatingPointData [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms) [ RUN ] ReferenceDataTest.HandlesPresenceChecks [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms) [ RUN ] ReferenceDataTest.HandlesStringBlockData [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms) [ RUN ] ReferenceDataTest.HandlesVectorData [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) [ RUN ] ReferenceDataTest.HandlesSequenceData [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms) [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) [ RUN ] ReferenceDataTest.HandlesIncorrectData [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) [ RUN ] ReferenceDataTest.HandlesIncorrectDataType [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) [ RUN ] ReferenceDataTest.HandlesMissingData [ OK ] ReferenceDataTest.HandlesMissingData (1 ms) [ RUN ] ReferenceDataTest.HandlesUncheckedData [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms) [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) [ RUN ] ReferenceDataTest.HandlesAnys [ OK ] ReferenceDataTest.HandlesAnys (1 ms) [ RUN ] ReferenceDataTest.HandlesKeyValueTree [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms) [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms) [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms) [ RUN ] ReferenceDataTest.HandlesEmptyStrings [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) [ RUN ] ReferenceDataTest.HandlesMultipleNullIds [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) [ RUN ] ReferenceDataTest.HandlesReadingValues [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms) [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms) [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms) [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms) [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms) [----------] 34 tests from ReferenceDataTest (48 ms total) [----------] 7 tests from FloatingPointDifferenceTest [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) [ RUN ] FloatingPointDifferenceTest.HandlesNaN [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) [----------] 4 tests from FloatingPointToleranceTest [ RUN ] FloatingPointToleranceTest.UlpTolerance [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) [----------] 4 tests from FloatingPointToleranceTest (0 ms total) [----------] 4 tests from XvgTests [ RUN ] XvgTests.CreateFile [ OK ] XvgTests.CreateFile (1 ms) [ RUN ] XvgTests.CheckMissing [ OK ] XvgTests.CheckMissing (1 ms) [ RUN ] XvgTests.CheckExtra [ OK ] XvgTests.CheckExtra (1 ms) [ RUN ] XvgTests.ReadIncorrect [ OK ] XvgTests.ReadIncorrect (1 ms) [----------] 4 tests from XvgTests (5 ms total) [----------] Global test environment tear-down [==========] 59 tests from 5 test suites ran. (69 ms total) [ PASSED ] 59 tests. Test time = 0.74 sec ---------------------------------------------------------- Test Passed. "TestUtilsUnitTests" end time: Feb 22 23:20 EST "TestUtilsUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 14/90 Testing: TestUtilsMpiUnitTests 14/90 Test: TestUtilsMpiUnitTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/testutils-mpi-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TestUtilsMpiUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/testutils/tests "TestUtilsMpiUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from MpiSelfTest [ RUN ] MpiSelfTest.Runs [ OK ] MpiSelfTest.Runs (0 ms) [----------] 1 test from MpiSelfTest (0 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (0 ms total) [ PASSED ] 1 test. Test time = 0.75 sec ---------------------------------------------------------- Test Passed. "TestUtilsMpiUnitTests" end time: Feb 22 23:20 EST "TestUtilsMpiUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 15/90 Testing: UtilityUnitTests 15/90 Test: UtilityUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/utility-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/UtilityUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/utility/tests "UtilityUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 386 tests from 61 test suites. [----------] Global test environment set-up. [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.Move [ OK ] AllocatorTest/0.Move (0 ms) [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/0 (0 ms total) [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.Move [ OK ] AllocatorTest/1.Move (0 ms) [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/1 (0 ms total) [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.Move [ OK ] AllocatorTest/2.Move (0 ms) [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/2 (0 ms total) [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.Move [ OK ] AllocatorTest/3.Move (0 ms) [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/3 (0 ms total) [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/4.Move [ OK ] AllocatorTest/4.Move (0 ms) [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/4 (0 ms total) [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/5.Move [ OK ] AllocatorTest/5.Move (0 ms) [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) [----------] 5 tests from AllocatorTest/5 (0 ms total) [----------] 1 test from AllocatorUntypedTest [ RUN ] AllocatorUntypedTest.Comparison [ OK ] AllocatorUntypedTest.Comparison (0 ms) [----------] 1 test from AllocatorUntypedTest (0 ms total) [----------] 4 tests from EmptyArrayRefTest [ RUN ] EmptyArrayRefTest.IsEmpty [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) [----------] 4 tests from EmptyArrayRefTest (0 ms total) [----------] 1 test from EmptyConstArrayRefTest [ RUN ] EmptyConstArrayRefTest.IsEmpty [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) [----------] 1 test from EmptyConstArrayRefTest (0 ms total) [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/0 (0 ms total) [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/1 (0 ms total) [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/2 (0 ms total) [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/3 (0 ms total) [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/4 (0 ms total) [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/5 (0 ms total) [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/6 (0 ms total) [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/7 (0 ms total) [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/8 (0 ms total) [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/9 (0 ms total) [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/10 (0 ms total) [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/11 (0 ms total) [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/12 (0 ms total) [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/13 (0 ms total) [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/14 (0 ms total) [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/15 (0 ms total) [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/16 (0 ms total) [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/17 (0 ms total) [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/18 (0 ms total) [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) [----------] 9 tests from ArrayRefTest/19 (0 ms total) [----------] 2 tests from CStringUtilityTest [ RUN ] CStringUtilityTest.CaseInsensitiveComparison [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) [----------] 2 tests from CStringUtilityTest (0 ms total) [----------] 2 tests from DefaultInitializationAllocator [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) [----------] 2 tests from DefaultInitializationAllocator (0 ms total) [----------] 4 tests from EnumerationHelpersTest [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) [----------] 4 tests from EnumerationHelpersTest (0 ms total) [----------] 9 tests from FixedCapacityVectorTest [ RUN ] FixedCapacityVectorTest.IsEmpty [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) [ RUN ] FixedCapacityVectorTest.PushWorks [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) [ RUN ] FixedCapacityVectorTest.PopWorks [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) [ RUN ] FixedCapacityVectorTest.ClearWorks [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) [ RUN ] FixedCapacityVectorTest.AtThrows [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) [ RUN ] FixedCapacityVectorTest.IteratorWorks [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) [----------] 9 tests from FixedCapacityVectorTest (0 ms total) [----------] 5 tests from InMemorySerializerTest [ RUN ] InMemorySerializerTest.Roundtrip [ OK ] InMemorySerializerTest.Roundtrip (0 ms) [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) [ RUN ] InMemorySerializerTest.SizeIsCorrect [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) [----------] 5 tests from InMemorySerializerTest (0 ms total) [----------] 4 tests from KeyValueTreeSerializerTest [ RUN ] KeyValueTreeSerializerTest.EmptyTree [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) [ RUN ] KeyValueTreeSerializerTest.SimpleObject [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total) [----------] 6 tests from TreeValueTransformTest [ RUN ] TreeValueTransformTest.SimpleTransforms [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) [ RUN ] TreeValueTransformTest.SimpleTransformsToObject [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) [ RUN ] TreeValueTransformTest.ObjectFromString [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) [ RUN ] TreeValueTransformTest.ScopedTransformRules [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) [----------] 6 tests from TreeValueTransformTest (3 ms total) [----------] 1 test from TreeValueTransformErrorTest [ RUN ] TreeValueTransformErrorTest.ConversionError [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) [----------] 1 test from TreeValueTransformErrorTest (0 ms total) [----------] 9 tests from ListOfLists [ RUN ] ListOfLists.EmptyListOfListsWorks [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) [ RUN ] ListOfLists.AppendWorks [ OK ] ListOfLists.AppendWorks (0 ms) [ RUN ] ListOfLists.EmptyListWorks [ OK ] ListOfLists.EmptyListWorks (0 ms) [ RUN ] ListOfLists.AppendAccessWorks [ OK ] ListOfLists.AppendAccessWorks (0 ms) [ RUN ] ListOfLists.ClearWorks [ OK ] ListOfLists.ClearWorks (0 ms) [ RUN ] ListOfLists.OutOfRangeAccessThrows [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) [ RUN ] ListOfLists.FrontAndBackWork [ OK ] ListOfLists.FrontAndBackWork (0 ms) [ RUN ] ListOfLists.ExtractsAndRestores [ OK ] ListOfLists.ExtractsAndRestores (0 ms) [ RUN ] ListOfLists.AppendsListOfListsWithOffset [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) [----------] 9 tests from ListOfLists (0 ms total) [----------] 7 tests from LoggerTest [ RUN ] LoggerTest.EmptyLoggerWorks [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) [ RUN ] LoggerTest.LogsToStream [ OK ] LoggerTest.LogsToStream (0 ms) [ RUN ] LoggerTest.LogsToFile [ OK ] LoggerTest.LogsToFile (1 ms) [ RUN ] LoggerTest.LevelFilteringWorks [ OK ] LoggerTest.LevelFilteringWorks (0 ms) [ RUN ] LoggerTest.LogsToMultipleStreams [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) [ RUN ] LoggerTest.LogsToMultipleFiles [ OK ] LoggerTest.LogsToMultipleFiles (6 ms) [ RUN ] LoggerTest.LogsToStreamAndFile [ OK ] LoggerTest.LogsToStreamAndFile (1 ms) [----------] 7 tests from LoggerTest (11 ms total) [----------] 4 tests from MDModulesNotifierTest [ RUN ] MDModulesNotifierTest.AddConsumer [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) [----------] 4 tests from MDModulesNotifierTest (0 ms total) [----------] 7 tests from MessageStringCollectorTest [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) [ RUN ] MessageStringCollectorTest.CanAddStringMessages [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) [ RUN ] MessageStringCollectorTest.CanMoveConstruct [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) [ RUN ] MessageStringCollectorTest.CanMoveAssign [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) [----------] 7 tests from MessageStringCollectorTest (0 ms total) [----------] 1 test from PathTest [ RUN ] PathTest.StripSourcePrefixWorks [ OK ] PathTest.StripSourcePrefixWorks (0 ms) [----------] 1 test from PathTest (0 ms total) [----------] 2 tests from PhysicalNodeCommunicatorTest [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) [----------] 5 tests from Range [ RUN ] Range.EmptyRangeWorks [ OK ] Range.EmptyRangeWorks (0 ms) [ RUN ] Range.NonEmptyRangeWorks [ OK ] Range.NonEmptyRangeWorks (0 ms) [ RUN ] Range.BeginEnd [ OK ] Range.BeginEnd (0 ms) [ RUN ] Range.IsInRangeWorks [ OK ] Range.IsInRangeWorks (0 ms) [ RUN ] Range.IteratorWorks [ OK ] Range.IteratorWorks (0 ms) [----------] 5 tests from Range (0 ms total) [----------] 7 tests from StringConvert [ RUN ] StringConvert.NoResultFromEptyString [ OK ] StringConvert.NoResultFromEptyString (0 ms) [ RUN ] StringConvert.ThreeFloatsSuccessfully [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) [ RUN ] StringConvert.OneIntSucessfully [ OK ] StringConvert.OneIntSucessfully (0 ms) [ RUN ] StringConvert.FloatAsStringToIntArrayThrows [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) [ RUN ] StringConvert.ThrowsWhenWrongSize [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) [----------] 7 tests from StringConvert (0 ms total) [----------] 7 tests from StringToEnumValueConverterTest [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) [----------] 9 tests from StringUtilityTest [ RUN ] StringUtilityTest.StartsWith [ OK ] StringUtilityTest.StartsWith (0 ms) [ RUN ] StringUtilityTest.EndsWith [ OK ] StringUtilityTest.EndsWith (0 ms) [ RUN ] StringUtilityTest.StripSuffixIfPresent [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) [ RUN ] StringUtilityTest.StripString [ OK ] StringUtilityTest.StripString (0 ms) [ RUN ] StringUtilityTest.SplitString [ OK ] StringUtilityTest.SplitString (0 ms) [ RUN ] StringUtilityTest.SplitDelimitedString [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) [ RUN ] StringUtilityTest.CanCompareCaseInsensitive [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) [----------] 9 tests from StringUtilityTest (0 ms total) [----------] 2 tests from FormatStringTest [ RUN ] FormatStringTest.HandlesBasicFormatting [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) [ RUN ] FormatStringTest.HandlesLongStrings [ OK ] FormatStringTest.HandlesLongStrings (0 ms) [----------] 2 tests from FormatStringTest (0 ms total) [----------] 1 test from StringFormatterTest [ RUN ] StringFormatterTest.HandlesBasicFormatting [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) [----------] 1 test from StringFormatterTest (0 ms total) [----------] 1 test from formatAndJoinTest [ RUN ] formatAndJoinTest.Works [ OK ] formatAndJoinTest.Works (0 ms) [----------] 1 test from formatAndJoinTest (0 ms total) [----------] 1 test from JoinStringsTest [ RUN ] JoinStringsTest.Works [ OK ] JoinStringsTest.Works (0 ms) [----------] 1 test from JoinStringsTest (0 ms total) [----------] 6 tests from ReplaceAllTest [ RUN ] ReplaceAllTest.HandlesEmptyStrings [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) [ RUN ] ReplaceAllTest.HandlesNoMatches [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) [ RUN ] ReplaceAllTest.HandlesMultipleMatches [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) [ RUN ] ReplaceAllTest.HandlesWordBoundaries [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) [----------] 6 tests from ReplaceAllTest (0 ms total) [----------] 10 tests from TextLineWrapperTest [ RUN ] TextLineWrapperTest.HandlesEmptyStrings [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) [ RUN ] TextLineWrapperTest.WrapsCorrectly [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) [ RUN ] TextLineWrapperTest.HandlesIndent [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) [ RUN ] TextLineWrapperTest.HandlesHangingIndent [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) [----------] 10 tests from TextLineWrapperTest (4 ms total) [----------] 3 tests from TemplateMPTest [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) [----------] 3 tests from TemplateMPTest (0 ms total) [----------] 6 tests from TextWriterTest [ RUN ] TextWriterTest.WritesLines [ OK ] TextWriterTest.WritesLines (0 ms) [ RUN ] TextWriterTest.WritesLinesInParts [ OK ] TextWriterTest.WritesLinesInParts (0 ms) [ RUN ] TextWriterTest.WritesWrappedLines [ OK ] TextWriterTest.WritesWrappedLines (0 ms) [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) [ RUN ] TextWriterTest.TracksNewlines [ OK ] TextWriterTest.TracksNewlines (0 ms) [ RUN ] TextWriterTest.PreservesTrailingWhitespace [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) [----------] 6 tests from TextWriterTest (3 ms total) [----------] 1 test from TypeTraitsTest [ RUN ] TypeTraitsTest.IsIntegralConstant [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) [----------] 1 test from TypeTraitsTest (0 ms total) [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) [----------] 11 tests from WithInputPaths/PathSearchTest [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) [----------] 11 tests from WithInputPaths/PathSearchTest (6 ms total) [----------] 7 tests from ParsesLinesDifferently/TextReaderTest [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) [----------] Global test environment tear-down [==========] 386 tests from 61 test suites ran. (35 ms total) [ PASSED ] 386 tests. YOU HAVE 1 DISABLED TEST Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "UtilityUnitTests" end time: Feb 22 23:20 EST "UtilityUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 16/90 Testing: UtilityMpiUnitTests 16/90 Test: UtilityMpiUnitTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/utility-mpi-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/UtilityMpiUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/utility/tests "UtilityMpiUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 2 tests from 1 test suite. [----------] Global test environment set-up. [----------] 2 tests from PhysicalNodeCommunicatorTest [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) [----------] Global test environment tear-down [==========] 2 tests from 1 test suite ran. (0 ms total) [ PASSED ] 2 tests. Test time = 0.81 sec ---------------------------------------------------------- Test Passed. "UtilityMpiUnitTests" end time: Feb 22 23:20 EST "UtilityMpiUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 17/90 Testing: GmxlibTests 17/90 Test: GmxlibTests Command: "${WORKDIR}/gromacs-2022/build/bin/nonbonded-fep-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxlibTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxlib/nonbonded/tests "GmxlibTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 72 tests from 1 test suite. [----------] Global test environment set-up. [----------] 72 tests from NBInteraction/NonbondedFepTest [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (1 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) [----------] 72 tests from NBInteraction/NonbondedFepTest (42 ms total) [----------] Global test environment tear-down [==========] 72 tests from 1 test suite ran. (42 ms total) [ PASSED ] 72 tests. Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "GmxlibTests" end time: Feb 22 23:20 EST "GmxlibTests" time elapsed: 00:00:00 ---------------------------------------------------------- 18/90 Testing: MdlibUnitTest 18/90 Test: MdlibUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/mdlib-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdlibUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests "MdlibUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 155 tests from 17 test suites. [----------] Global test environment set-up. [----------] 1 test from VerletBufferConstraintTest [ RUN ] VerletBufferConstraintTest.EqualMasses [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) [----------] 1 test from VerletBufferConstraintTest (0 ms total) [----------] 6 tests from CalcvirTest [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) [----------] 6 tests from CalcvirTest (3 ms total) [----------] 2 tests from PrEbinTest [ RUN ] PrEbinTest.HandlesAverages [ OK ] PrEbinTest.HandlesAverages (2 ms) [ RUN ] PrEbinTest.HandlesEmptyAverages [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms) [----------] 2 tests from PrEbinTest (4 ms total) [----------] 3 tests from EnergyDriftTracker [ RUN ] EnergyDriftTracker.emptyWorks [ OK ] EnergyDriftTracker.emptyWorks (0 ms) [ RUN ] EnergyDriftTracker.onePointWorks [ OK ] EnergyDriftTracker.onePointWorks (0 ms) [ RUN ] EnergyDriftTracker.manyPointsWorks [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) [----------] 3 tests from EnergyDriftTracker (0 ms total) [----------] 4 tests from ShakeTest [ RUN ] ShakeTest.ConstrainsOneBond [ OK ] ShakeTest.ConstrainsOneBond (0 ms) [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) [----------] 4 tests from ShakeTest (0 ms total) [----------] 1 test from NullSignalTest [ RUN ] NullSignalTest.NullSignallerWorks [ OK ] NullSignalTest.NullSignallerWorks (0 ms) [----------] 1 test from NullSignalTest (0 ms total) [----------] 7 tests from SignalTest [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) [----------] 7 tests from SignalTest (0 ms total) [----------] 13 tests from UpdateGroupsTest [ RUN ] UpdateGroupsTest.WithEthaneUA [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) [ RUN ] UpdateGroupsTest.WithMethane [ OK ] UpdateGroupsTest.WithMethane (0 ms) [ RUN ] UpdateGroupsTest.WithEthane [ OK ] UpdateGroupsTest.WithEthane (0 ms) [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) [ RUN ] UpdateGroupsTest.WithWaterThreeSite [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) [ RUN ] UpdateGroupsTest.WithWaterFourSite [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) [ RUN ] UpdateGroupsTest.WithWaterFlexAngle [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) [ RUN ] UpdateGroupsTest.WithTwoMoltypes [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) [----------] 13 tests from UpdateGroupsTest (0 ms total) [----------] 1 test from UpdateGroupsCog [ RUN ] UpdateGroupsCog.ComputesCogs [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) [----------] 1 test from UpdateGroupsCog (0 ms total) [----------] 2 tests from WholeMoleculeTransform [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) [ RUN ] WholeMoleculeTransform.HandlesReordering [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) [----------] 2 tests from WholeMoleculeTransform (0 ms total) [----------] 14 tests from WithParameters/ConstraintsTest [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (3 ms) [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (3 ms) [----------] 14 tests from WithParameters/ConstraintsTest (15 ms total) [----------] 11 tests from WithParameters/EnergyOutputTest [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (5 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (4 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (3 ms) [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 Opened ${WORKDIR}/gromacs-2022/build/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (3 ms) [----------] 11 tests from WithParameters/EnergyOutputTest (43 ms total) [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) [----------] 23 tests from WithParameters/FreeEnergyParameterTest [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) [----------] 16 tests from WithParameters/LeapFrogTest [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) [----------] 16 tests from WithParameters/LeapFrogTest (17 ms total) [----------] 13 tests from WithParameters/SettleTest [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) [----------] 13 tests from WithParameters/SettleTest (10 ms total) [----------] Global test environment tear-down [==========] 155 tests from 17 test suites ran. (97 ms total) [ PASSED ] 155 tests. Test time = 0.82 sec ---------------------------------------------------------- Test Passed. "MdlibUnitTest" end time: Feb 22 23:20 EST "MdlibUnitTest" time elapsed: 00:00:00 ---------------------------------------------------------- 19/90 Testing: AwhTest 19/90 Test: AwhTest Command: "${WORKDIR}/gromacs-2022/build/bin/awh-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/AwhTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/awh/tests "AwhTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 20 tests from 7 test suites. [----------] Global test environment set-up. [----------] 3 tests from SerializationTest [ RUN ] SerializationTest.CanSerializeDimParams [ OK ] SerializationTest.CanSerializeDimParams (0 ms) [ RUN ] SerializationTest.CanSerializeBiasParams [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) [ RUN ] SerializationTest.CanSerializeAwhParams [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) [----------] 3 tests from SerializationTest (0 ms total) [----------] 1 test from BiasTest [ RUN ] BiasTest.DetectsCovering [ OK ] BiasTest.DetectsCovering (0 ms) [----------] 1 test from BiasTest (0 ms total) [----------] 1 test from biasGridTest [ RUN ] biasGridTest.neighborhood [ OK ] biasGridTest.neighborhood (0 ms) [----------] 1 test from biasGridTest (0 ms total) [----------] 1 test from BiasFepLambdaStateTest [ RUN ] BiasFepLambdaStateTest.DetectsCovering [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) [----------] 1 test from BiasFepLambdaStateTest (1 ms total) [----------] 8 tests from WithParameters/BiasTest [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) [----------] 8 tests from WithParameters/BiasTest (6 ms total) [----------] 2 tests from WithParameters/BiasStateTest [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) [----------] 4 tests from WithParameters/BiasFepLambdaStateTest [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (16 ms total) [----------] Global test environment tear-down [==========] 20 tests from 7 test suites ran. (27 ms total) [ PASSED ] 20 tests. Test time = 0.71 sec ---------------------------------------------------------- Test Passed. "AwhTest" end time: Feb 22 23:20 EST "AwhTest" time elapsed: 00:00:00 ---------------------------------------------------------- 20/90 Testing: DensityFittingAppliedForcesUnitTest 20/90 Test: DensityFittingAppliedForcesUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/density_fitting_applied_forces-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/densityfitting/tests "DensityFittingAppliedForcesUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 18 tests from 4 test suites. [----------] Global test environment set-up. [----------] 2 tests from DensityFittingTest [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) [ RUN ] DensityFittingTest.SingleAtom [ OK ] DensityFittingTest.SingleAtom (1 ms) [----------] 2 tests from DensityFittingTest (1 ms total) [----------] 7 tests from DensityFittingAmplitudeLookupTest [ RUN ] DensityFittingAmplitudeLookupTest.Unity [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.Charge [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.Masses [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) [----------] 1 test from DensityFittingForceProviderState [ RUN ] DensityFittingForceProviderState.RoundTripSaving [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) [----------] 1 test from DensityFittingForceProviderState (0 ms total) [----------] 8 tests from DensityFittingOptionsTest [ RUN ] DensityFittingOptionsTest.DefaultParameters [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) [ RUN ] DensityFittingOptionsTest.OptionSetsActive [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) [ RUN ] DensityFittingOptionsTest.InternalsToKvt [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) [ RUN ] DensityFittingOptionsTest.KvtToInternal [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) [----------] 8 tests from DensityFittingOptionsTest (0 ms total) [----------] Global test environment tear-down [==========] 18 tests from 4 test suites ran. (2 ms total) [ PASSED ] 18 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "DensityFittingAppliedForcesUnitTest" end time: Feb 22 23:20 EST "DensityFittingAppliedForcesUnitTest" time elapsed: 00:00:00 ---------------------------------------------------------- 21/90 Testing: QMMMAppliedForcesUnitTest 21/90 Test: QMMMAppliedForcesUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/qmmm_applied_forces-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests "QMMMAppliedForcesUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 21 tests from 5 test suites. [----------] Global test environment set-up. [----------] 3 tests from QMMMInputGeneratorTest [ RUN ] QMMMInputGeneratorTest.CanConstruct [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (1351 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) [----------] 3 tests from QMMMInputGeneratorTest (1352 ms total) [----------] 7 tests from QMMMTopologyPreprocessorTest [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (1 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022 (single precision) Setting the LD random seed to -41955713 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (13 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022 (single precision) Setting the LD random seed to -641861699 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (9 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022 (single precision) Setting the LD random seed to -1074960514 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (9 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 63.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 129.093 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022 (single precision) Setting the LD random seed to -268442371 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.013 nm Set rlist, assuming 4x4 atom pair-list, to 1.008 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (15 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 3 [file unknown]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 42.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 193.640 K for determining the Verlet buffer size NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022 (single precision) Setting the LD random seed to -359991507 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning all bonds into constraints... Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K Calculated rlist for 1x1 atom pair-list as 1.015 nm, buffer size 0.015 nm Set rlist, assuming 4x4 atom pair-list, to 1.009 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (14 ms) [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Number of degrees of freedom in T-Coupling group rest is 45.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022 (single precision) Setting the LD random seed to -1820337169 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (9 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (72 ms total) [----------] 9 tests from QMMMOptionsTest [ RUN ] QMMMOptionsTest.DefaultParameters [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) [ RUN ] QMMMOptionsTest.OptionSetsActive [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) [ RUN ] QMMMOptionsTest.CP2KInputProcessing [ OK ] QMMMOptionsTest.CP2KInputProcessing (1 ms) [----------] 9 tests from QMMMOptionsTest (4 ms total) [----------] 1 test from QMMMForceProviderTest [ RUN ] QMMMForceProviderTest.CanConstructOrNot [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) [----------] 1 test from QMMMForceProviderTest (0 ms total) [----------] 1 test from QMMMTest [ RUN ] QMMMTest.ForceProviderLackingInputThrows [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) [----------] 1 test from QMMMTest (0 ms total) [----------] Global test environment tear-down [==========] 21 tests from 5 test suites ran. (1430 ms total) [ PASSED ] 21 tests. Test time = 2.10 sec ---------------------------------------------------------- Test Passed. "QMMMAppliedForcesUnitTest" end time: Feb 22 23:20 EST "QMMMAppliedForcesUnitTest" time elapsed: 00:00:02 ---------------------------------------------------------- 22/90 Testing: AppliedForcesUnitTest 22/90 Test: AppliedForcesUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/applied_forces-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/AppliedForcesUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/applied_forces/tests "AppliedForcesUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 3 tests from 1 test suite. [----------] Global test environment set-up. [----------] 3 tests from ElectricFieldTest [ RUN ] ElectricFieldTest.Static [ OK ] ElectricFieldTest.Static (0 ms) [ RUN ] ElectricFieldTest.Oscillating [ OK ] ElectricFieldTest.Oscillating (0 ms) [ RUN ] ElectricFieldTest.Pulsed [ OK ] ElectricFieldTest.Pulsed (0 ms) [----------] 3 tests from ElectricFieldTest (0 ms total) [----------] Global test environment tear-down [==========] 3 tests from 1 test suite ran. (0 ms total) [ PASSED ] 3 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "AppliedForcesUnitTest" end time: Feb 22 23:20 EST "AppliedForcesUnitTest" time elapsed: 00:00:00 ---------------------------------------------------------- 23/90 Testing: ListedForcesTest 23/90 Test: ListedForcesTest Command: "${WORKDIR}/gromacs-2022/build/bin/listed_forces-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/ListedForcesTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/listed_forces/tests "ListedForcesTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 132 tests from 9 test suites. [----------] Global test environment set-up. [----------] 24 tests from Bond/ListedForcesTest [ RUN ] Bond/ListedForcesTest.Ifunc/0 [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/1 [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/2 [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/3 [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/4 [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/5 [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/6 [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/7 [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/8 [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/9 [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/10 [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/11 [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/12 [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/13 [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/14 [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/15 [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/16 [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/17 [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/18 [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/19 [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/20 [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/21 [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/22 [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) [ RUN ] Bond/ListedForcesTest.Ifunc/23 [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) [----------] 24 tests from Bond/ListedForcesTest (15 ms total) [----------] 33 tests from Angle/ListedForcesTest [ RUN ] Angle/ListedForcesTest.Ifunc/0 [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/1 [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/2 [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/3 [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/4 [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/5 [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/6 [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/7 [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/8 [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/9 [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/10 [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/11 [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/12 [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/13 [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/14 [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/15 [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/16 [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/17 [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/18 [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/19 [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/20 [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/21 [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/22 [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/23 [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/24 [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/25 [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/26 [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/27 [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/28 [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/29 [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/30 [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/31 [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) [ RUN ] Angle/ListedForcesTest.Ifunc/32 [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) [----------] 33 tests from Angle/ListedForcesTest (20 ms total) [----------] 18 tests from Dihedral/ListedForcesTest [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) [----------] 18 tests from Dihedral/ListedForcesTest (11 ms total) [----------] 12 tests from Polarize/ListedForcesTest [ RUN ] Polarize/ListedForcesTest.Ifunc/0 [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/1 [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/2 [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/3 [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/4 [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/5 [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/6 [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/7 [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/8 [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/9 [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/10 [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) [ RUN ] Polarize/ListedForcesTest.Ifunc/11 [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) [----------] 12 tests from Polarize/ListedForcesTest (6 ms total) [----------] 18 tests from Restraints/ListedForcesTest [ RUN ] Restraints/ListedForcesTest.Ifunc/0 [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/1 [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/2 [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/3 [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/4 [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/5 [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/6 [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/7 [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/8 [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/9 [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/10 [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/11 [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/12 [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/13 [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/14 [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/15 [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/16 [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) [ RUN ] Restraints/ListedForcesTest.Ifunc/17 [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) [----------] 18 tests from Restraints/ListedForcesTest (10 ms total) [----------] 3 tests from BondZeroLength/ListedForcesTest [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total) [----------] 3 tests from AngleZero/ListedForcesTest [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total) [----------] 12 tests from 14Interaction/ListedForcesPairsTest [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) [----------] 12 tests from 14Interaction/ListedForcesPairsTest (7 ms total) [----------] 9 tests from PosResBasicTest/PositionRestraintsTest [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (5 ms total) [----------] Global test environment tear-down [==========] 132 tests from 9 test suites ran. (80 ms total) [ PASSED ] 132 tests. Test time = 0.75 sec ---------------------------------------------------------- Test Passed. "ListedForcesTest" end time: Feb 22 23:20 EST "ListedForcesTest" time elapsed: 00:00:00 ---------------------------------------------------------- 24/90 Testing: NbnxmTests 24/90 Test: NbnxmTests Command: "${WORKDIR}/gromacs-2022/build/bin/nbnxm-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/NbnxmTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/nbnxm/tests "NbnxmTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 18 tests from 1 test suite. [----------] Global test environment set-up. [----------] 18 tests from KernelSetupTest [ RUN ] KernelSetupTest.getCoulombKernelTypeRF [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) [ RUN ] KernelSetupTest.getCoulombKernelTypeCut [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) [ RUN ] KernelSetupTest.getCoulombKernelTypeTable [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) [----------] 18 tests from KernelSetupTest (0 ms total) [----------] Global test environment tear-down [==========] 18 tests from 1 test suite ran. (0 ms total) [ PASSED ] 18 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "NbnxmTests" end time: Feb 22 23:20 EST "NbnxmTests" time elapsed: 00:00:00 ---------------------------------------------------------- 25/90 Testing: CommandLineUnitTests 25/90 Test: CommandLineUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/commandline-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/CommandLineUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/commandline/tests "CommandLineUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 60 tests from 7 test suites. [----------] Global test environment set-up. [----------] 3 tests from CommandLineHelpModuleTest [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) [ RUN ] CommandLineHelpModuleTest.ExportsHelp [ OK ] CommandLineHelpModuleTest.ExportsHelp (2 ms) [----------] 3 tests from CommandLineHelpModuleTest (5 ms total) [----------] 7 tests from CommandLineHelpWriterTest [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesHelpText [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) [----------] 7 tests from CommandLineHelpWriterTest (4 ms total) [----------] 6 tests from CommandLineModuleManagerTest [ RUN ] CommandLineModuleManagerTest.RunsModule [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) [----------] 13 tests from CommandLineParserTest [ RUN ] CommandLineParserTest.HandlesSingleValues [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) [ RUN ] CommandLineParserTest.HandlesNegativeNumbers [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) [ RUN ] CommandLineParserTest.HandlesString [ OK ] CommandLineParserTest.HandlesString (0 ms) [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) [ RUN ] CommandLineParserTest.HandlesSkipUnknown [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) [ RUN ] CommandLineParserTest.CanAllowPositionalArguments [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) [----------] 13 tests from CommandLineParserTest (0 ms total) [----------] 6 tests from CommandLineProgramContextTest [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) [----------] 6 tests from CommandLineProgramContextTest (1 ms total) [----------] 3 tests from OutputNamesTest [ RUN ] OutputNamesTest.CanBeSuffixed [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) [ RUN ] OutputNamesTest.HasSuffixFromNoAppend [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) [ RUN ] OutputNamesTest.CanHavePartNumberAdded [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) [----------] 3 tests from OutputNamesTest (0 ms total) [----------] 22 tests from ParseCommonArgsTest [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesInt64Args [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) [ RUN ] ParseCommonArgsTest.ParsesRealArgs [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesStringArgs [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) [ RUN ] ParseCommonArgsTest.ParsesVectorArgs [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesTimeArgs [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) [ RUN ] ParseCommonArgsTest.ParsesEnumArgs [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesFileArgs [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms) [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms) [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms) [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms) [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (6 ms) [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (4 ms) [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) [----------] 22 tests from ParseCommonArgsTest (17 ms total) [----------] Global test environment tear-down [==========] 60 tests from 7 test suites ran. (30 ms total) [ PASSED ] 60 tests. Test time = 0.70 sec ---------------------------------------------------------- Test Passed. "CommandLineUnitTests" end time: Feb 22 23:20 EST "CommandLineUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 26/90 Testing: DomDecTests 26/90 Test: DomDecTests Command: "${WORKDIR}/gromacs-2022/build/bin/domdec-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/DomDecTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/domdec/tests "DomDecTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 9 tests from 2 test suites. [----------] Global test environment set-up. [----------] 7 tests from HashedMap [ RUN ] HashedMap.InsertsFinds [ OK ] HashedMap.InsertsFinds (0 ms) [ RUN ] HashedMap.NegativeKeysWork [ OK ] HashedMap.NegativeKeysWork (0 ms) [ RUN ] HashedMap.InsertsErases [ OK ] HashedMap.InsertsErases (0 ms) [ RUN ] HashedMap.InsertsOrAssigns [ OK ] HashedMap.InsertsOrAssigns (0 ms) [ RUN ] HashedMap.Clears [ OK ] HashedMap.Clears (0 ms) [ RUN ] HashedMap.LinkedEntries [ OK ] HashedMap.LinkedEntries (0 ms) [ RUN ] HashedMap.ResizesTable [ OK ] HashedMap.ResizesTable (0 ms) [----------] 7 tests from HashedMap (0 ms total) [----------] 2 tests from LocalAtomSetManager [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) [----------] 2 tests from LocalAtomSetManager (0 ms total) [----------] Global test environment tear-down [==========] 9 tests from 2 test suites ran. (0 ms total) [ PASSED ] 9 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "DomDecTests" end time: Feb 22 23:20 EST "DomDecTests" time elapsed: 00:00:00 ---------------------------------------------------------- 27/90 Testing: DomDecMpiTests 27/90 Test: DomDecMpiTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "4" "${WORKDIR}/gromacs-2022/build/bin/domdec-mpi-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/DomDecMpiTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/domdec/tests "DomDecMpiTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 4 tests from 1 test suite. [----------] Global test environment set-up. [----------] 4 tests from HaloExchangeTest [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) [----------] 4 tests from HaloExchangeTest (0 ms total) [----------] Global test environment tear-down [==========] 4 tests from 1 test suite ran. (0 ms total) [ PASSED ] 4 tests. Test time = 1.24 sec ---------------------------------------------------------- Test Passed. "DomDecMpiTests" end time: Feb 22 23:20 EST "DomDecMpiTests" time elapsed: 00:00:01 ---------------------------------------------------------- 28/90 Testing: EwaldUnitTests 28/90 Test: EwaldUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/ewald-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/EwaldUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/ewald/tests "EwaldUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 407 tests from 9 test suites. [----------] Global test environment set-up. [----------] 6 tests from SeparatePmeRanksPermittedTest [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) [----------] 108 tests from Pme_SplineAndSpreadTest [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (2 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) [----------] 108 tests from Pme_SplineAndSpreadTest (119 ms total) [----------] 64 tests from Pme_SolveTest [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [----------] 64 tests from Pme_SolveTest (24 ms total) [----------] 32 tests from PmeDiffEwaldQ_SolveTest [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [----------] 32 tests from PmeDiffEwaldQ_SolveTest (10 ms total) [----------] 32 tests from PmeDiffEwaldLJ_SolveTest [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (12 ms total) [----------] 64 tests from PmeDiffEps_SolveTest [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy ${WORKDIR}/gromacs-2022/src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped Test is being skipped because: CPU PME solve does not implement XYZ grid ordering [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) [----------] 64 tests from PmeDiffEps_SolveTest (23 ms total) [----------] 72 tests from Pme_GatherTest [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (3 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) [----------] 72 tests from Pme_GatherTest (51 ms total) [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (0 ms) [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (3 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (26 ms total) [----------] Global test environment tear-down [==========] 407 tests from 9 test suites ran. (269 ms total) [ PASSED ] 311 tests. [ SKIPPED ] 96 tests, listed below: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy Test time = 0.99 sec ---------------------------------------------------------- Test Passed. "EwaldUnitTests" end time: Feb 22 23:20 EST "EwaldUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 29/90 Testing: FFTUnitTests 29/90 Test: FFTUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/fft-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/FFTUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/fft/tests "FFTUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 15 tests from 4 test suites. [----------] Global test environment set-up. [----------] 2 tests from ManyFFTTest [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) [ RUN ] ManyFFTTest.Real1DLength48Multi5Test [ OK ] ManyFFTTest.Real1DLength48Multi5Test (15 ms) [----------] 2 tests from ManyFFTTest (22 ms total) [----------] 1 test from FFTTest [ RUN ] FFTTest.Real2DLength18_15Test [ OK ] FFTTest.Real2DLength18_15Test (13 ms) [----------] 1 test from FFTTest (14 ms total) [----------] 10 tests from 7_8_25_36_60/FFTTest1D [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (9 ms) [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (13 ms) [----------] 10 tests from 7_8_25_36_60/FFTTest1D (33 ms total) [----------] 2 tests from Works/ParameterizedFFTTest3D [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) [----------] 2 tests from Works/ParameterizedFFTTest3D (3 ms total) [----------] Global test environment tear-down [==========] 15 tests from 4 test suites ran. (73 ms total) [ PASSED ] 15 tests. Test time = 0.78 sec ---------------------------------------------------------- Test Passed. "FFTUnitTests" end time: Feb 22 23:20 EST "FFTUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 30/90 Testing: GpuUtilsUnitTests 30/90 Test: GpuUtilsUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/gpu_utils-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GpuUtilsUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gpu_utils/tests "GpuUtilsUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 64 tests from 22 test suites. [----------] Global test environment set-up. [----------] 2 tests from ClfftInitializer [ RUN ] ClfftInitializer.SingleInitializationWorks [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) [ RUN ] ClfftInitializer.TwoInitializationsWork [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) [----------] 2 tests from ClfftInitializer (0 ms total) [----------] 1 test from DevicesAvailable [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) [----------] 1 test from DevicesAvailable (0 ms total) [----------] 1 test from DeviceStreamManagerTest [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) [----------] 1 test from DeviceStreamManagerTest (0 ms total) [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) [----------] 2 tests from HostAllocatorTest/0 (0 ms total) [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) [----------] 2 tests from HostAllocatorTest/1 (0 ms total) [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) [----------] 2 tests from HostAllocatorTest/2 (0 ms total) [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) [----------] 2 tests from HostAllocatorTest/3 (0 ms total) [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int [ RUN ] HostAllocatorTestNoMem/0.CreateVector [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) [ RUN ] HostAllocatorTestNoMem/0.Swap [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) [ RUN ] HostAllocatorTestNoMem/0.Comparison [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float [ RUN ] HostAllocatorTestNoMem/1.CreateVector [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) [ RUN ] HostAllocatorTestNoMem/1.Swap [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) [ RUN ] HostAllocatorTestNoMem/1.Comparison [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector [ RUN ] HostAllocatorTestNoMem/2.CreateVector [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) [ RUN ] HostAllocatorTestNoMem/2.Swap [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) [ RUN ] HostAllocatorTestNoMem/2.Comparison [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly [ RUN ] HostAllocatorTestNoMem/3.CreateVector [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) [ RUN ] HostAllocatorTestNoMem/3.Swap [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) [ RUN ] HostAllocatorTestNoMem/3.Comparison [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) [----------] 1 test from HostAllocatorUntypedTest [ RUN ] HostAllocatorUntypedTest.Comparison [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) [----------] 1 test from HostAllocatorUntypedTest (0 ms total) [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/0.Move [ OK ] AllocatorTest/0.Move (0 ms) [----------] 4 tests from AllocatorTest/0 (0 ms total) [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/1.Move [ OK ] AllocatorTest/1.Move (0 ms) [----------] 4 tests from AllocatorTest/1 (0 ms total) [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/2.Move [ OK ] AllocatorTest/2.Move (0 ms) [----------] 4 tests from AllocatorTest/2 (0 ms total) [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) [ RUN ] AllocatorTest/3.Move [ OK ] AllocatorTest/3.Move (0 ms) [----------] 4 tests from AllocatorTest/3 (0 ms total) [----------] Global test environment tear-down [==========] 64 tests from 22 test suites ran. (0 ms total) [ PASSED ] 64 tests. Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "GpuUtilsUnitTests" end time: Feb 22 23:20 EST "GpuUtilsUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 31/90 Testing: HardwareUnitTests 31/90 Test: HardwareUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/hardware-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/HardwareUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/hardware/tests "HardwareUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 21 tests from 9 test suites. [----------] Global test environment set-up. [----------] 1 test from CpuInfoTest [ RUN ] CpuInfoTest.SupportLevel [ OK ] CpuInfoTest.SupportLevel (1 ms) [----------] 1 test from CpuInfoTest (1 ms total) [----------] 4 tests from HardwareTopologyTest [ RUN ] HardwareTopologyTest.Execute [ OK ] HardwareTopologyTest.Execute (41 ms) [ RUN ] HardwareTopologyTest.HwlocExecute [ OK ] HardwareTopologyTest.HwlocExecute (33 ms) [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (43 ms) [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (32 ms) [----------] 4 tests from HardwareTopologyTest (151 ms total) [----------] 1 test from DevicesManagerTest [ RUN ] DevicesManagerTest.Serialization [ OK ] DevicesManagerTest.Serialization (0 ms) [----------] 1 test from DevicesManagerTest (0 ms total) [----------] 5 tests from XeonE52620/MockHardwareTopologyTest [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (5 ms) [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (2 ms) [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (2 ms) [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (2 ms) [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (2 ms) [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (15 ms total) [----------] 5 tests from Xeon4116/MockHardwareTopologyTest [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (4 ms) [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (2 ms) [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (2 ms) [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (2 ms) [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (2 ms) [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (13 ms total) [----------] 2 tests from Core12900K/MockHardwareTopologyTest [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (2 ms) [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (3 ms) [----------] 2 tests from Core12900K/MockHardwareTopologyTest (5 ms total) [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (18 ms) [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (18 ms total) [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (26 ms) [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (26 ms total) [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (38 ms) [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (38 ms total) [----------] Global test environment tear-down [==========] 21 tests from 9 test suites ran. (272 ms total) [ PASSED ] 21 tests. Test time = 0.95 sec ---------------------------------------------------------- Test Passed. "HardwareUnitTests" end time: Feb 22 23:20 EST "HardwareUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 32/90 Testing: MathUnitTests 32/90 Test: MathUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/math-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MathUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/math/tests "MathUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 300 tests from 38 test suites. [----------] Global test environment set-up. [----------] 1 test from EmptyArrayRefWithPaddingTest [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) [----------] 1 test from EmptyConstArrayRefWithPaddingTest [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) [----------] 11 tests from TranslateAndScaleTest [ RUN ] TranslateAndScaleTest.identityTransformation [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) [ RUN ] TranslateAndScaleTest.scalingIdentity [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) [ RUN ] TranslateAndScaleTest.scalingNonTrivial [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) [ RUN ] TranslateAndScaleTest.scalingInverseNoZero [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) [----------] 11 tests from TranslateAndScaleTest (0 ms total) [----------] 2 tests from AffineTransformationTest [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) [ RUN ] AffineTransformationTest.applyTransformationToVectors [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) [----------] 2 tests from AffineTransformationTest (0 ms total) [----------] 12 tests from DensitySimilarityTest [ RUN ] DensitySimilarityTest.InnerProductIsCorrect [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (11 ms) [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (9 ms) [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) [----------] 12 tests from DensitySimilarityTest (24 ms total) [----------] 6 tests from StructureSimilarityTest [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) [ RUN ] StructureSimilarityTest.YieldsCorrectRho [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) [----------] 6 tests from StructureSimilarityTest (0 ms total) [----------] 8 tests from ExponentialMovingAverage [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) [ RUN ] ExponentialMovingAverage.YieldsCorrectValue [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) [ RUN ] ExponentialMovingAverage.SetAverageCorrectly [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) [----------] 8 tests from ExponentialMovingAverage (0 ms total) [----------] 21 tests from FunctionTest [ RUN ] FunctionTest.StaticLog2 [ OK ] FunctionTest.StaticLog2 (0 ms) [ RUN ] FunctionTest.Log2I32Bit [ OK ] FunctionTest.Log2I32Bit (0 ms) [ RUN ] FunctionTest.Log2I64Bit [ OK ] FunctionTest.Log2I64Bit (0 ms) [ RUN ] FunctionTest.GreatestCommonDivisor [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) [ RUN ] FunctionTest.InvsqrtFloat [ OK ] FunctionTest.InvsqrtFloat (0 ms) [ RUN ] FunctionTest.InvsqrtDouble [ OK ] FunctionTest.InvsqrtDouble (0 ms) [ RUN ] FunctionTest.InvsqrtInteger [ OK ] FunctionTest.InvsqrtInteger (0 ms) [ RUN ] FunctionTest.InvcbrtFloat [ OK ] FunctionTest.InvcbrtFloat (0 ms) [ RUN ] FunctionTest.InvcbrtDouble [ OK ] FunctionTest.InvcbrtDouble (0 ms) [ RUN ] FunctionTest.InvcbrtInteger [ OK ] FunctionTest.InvcbrtInteger (0 ms) [ RUN ] FunctionTest.SixthrootFloat [ OK ] FunctionTest.SixthrootFloat (0 ms) [ RUN ] FunctionTest.SixthrootDouble [ OK ] FunctionTest.SixthrootDouble (0 ms) [ RUN ] FunctionTest.SixthrootInteger [ OK ] FunctionTest.SixthrootInteger (0 ms) [ RUN ] FunctionTest.InvsixthrootFloat [ OK ] FunctionTest.InvsixthrootFloat (0 ms) [ RUN ] FunctionTest.InvsixthrootDouble [ OK ] FunctionTest.InvsixthrootDouble (0 ms) [ RUN ] FunctionTest.InvsixthrootInteger [ OK ] FunctionTest.InvsixthrootInteger (0 ms) [ RUN ] FunctionTest.Powers [ OK ] FunctionTest.Powers (0 ms) [ RUN ] FunctionTest.ErfInvFloat [ OK ] FunctionTest.ErfInvFloat (0 ms) [ RUN ] FunctionTest.ErfInvDouble [ OK ] FunctionTest.ErfInvDouble (0 ms) [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) [----------] 21 tests from FunctionTest (9 ms total) [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) [----------] 4 tests from GaussianOn1DLattice [ RUN ] GaussianOn1DLattice.sumsCloseToOne [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) [ RUN ] GaussianOn1DLattice.isCorrect [ OK ] GaussianOn1DLattice.isCorrect (0 ms) [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) [----------] 4 tests from GaussianOn1DLattice (0 ms total) [----------] 9 tests from GaussTransformTest [ RUN ] GaussTransformTest.isZeroUponConstruction [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) [ RUN ] GaussTransformTest.isZeroAfterSettingZero [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) [ RUN ] GaussTransformTest.complementaryGaussAddToZero [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) [ RUN ] GaussTransformTest.view [ OK ] GaussTransformTest.view (0 ms) [----------] 9 tests from GaussTransformTest (0 ms total) [----------] 3 tests from DensityFittingForce [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) [ RUN ] DensityFittingForce.pullsTowardsDerivative [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) [----------] 3 tests from DensityFittingForce (0 ms total) [----------] 2 tests from InvertMatrixTest [ RUN ] InvertMatrixTest.IdentityIsImpotent [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) [ RUN ] InvertMatrixTest.ComputesInverse [ OK ] InvertMatrixTest.ComputesInverse (0 ms) [----------] 2 tests from InvertMatrixTest (0 ms total) [----------] 2 tests from InvertBoxMatrixTest [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) [----------] 2 tests from InvertBoxMatrixTest (0 ms total) [----------] 17 tests from MatrixTest [ RUN ] MatrixTest.canSetFromArray [ OK ] MatrixTest.canSetFromArray (0 ms) [ RUN ] MatrixTest.canSetStaticallyFromList [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) [ RUN ] MatrixTest.canConstructAndFill [ OK ] MatrixTest.canConstructAndFill (0 ms) [ RUN ] MatrixTest.canSetValues [ OK ] MatrixTest.canSetValues (0 ms) [ RUN ] MatrixTest.canCopyAssign [ OK ] MatrixTest.canCopyAssign (0 ms) [ RUN ] MatrixTest.canSwap [ OK ] MatrixTest.canSwap (0 ms) [ RUN ] MatrixTest.staticMultiDimArrayExtent [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) [ RUN ] MatrixTest.determinantWorks [ OK ] MatrixTest.determinantWorks (0 ms) [ RUN ] MatrixTest.noninvertableDeterminantIsZero [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) [ RUN ] MatrixTest.determinantOfDiagonalMatrix [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) [ RUN ] MatrixTest.traceWorks [ OK ] MatrixTest.traceWorks (0 ms) [ RUN ] MatrixTest.transposeWorks [ OK ] MatrixTest.transposeWorks (0 ms) [ RUN ] MatrixTest.transposeOfSymmetricMatrix [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) [ RUN ] MatrixTest.canCreateFromLegacyMatrix [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) [ RUN ] MatrixTest.canFillLegacyMatrix [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) [ RUN ] MatrixTest.IdentityMatrix [ OK ] MatrixTest.IdentityMatrix (0 ms) [ RUN ] MatrixTest.MatrixVectorMultiplication [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) [----------] 17 tests from MatrixTest (0 ms total) [----------] 25 tests from MultiDimArrayTest [ RUN ] MultiDimArrayTest.canConstructAndFillStatic [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) [ RUN ] MultiDimArrayTest.canSetValuesInStatic [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) [ RUN ] MultiDimArrayTest.canSetValuesInDynamic [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) [ RUN ] MultiDimArrayTest.canMoveConstructStatic [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) [ RUN ] MultiDimArrayTest.canMoveConstructDynamic [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) [ RUN ] MultiDimArrayTest.canMoveAssignStatic [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) [ RUN ] MultiDimArrayTest.canMoveAssignDynamic [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) [ RUN ] MultiDimArrayTest.canCopyConstructStatic [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) [ RUN ] MultiDimArrayTest.canCopyConstructDynamic [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) [ RUN ] MultiDimArrayTest.canCopyAssignStatic [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) [ RUN ] MultiDimArrayTest.canCopyAssignDynamic [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) [ RUN ] MultiDimArrayTest.canSwapStatic [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) [ RUN ] MultiDimArrayTest.canSwapDynamic [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) [ RUN ] MultiDimArrayTest.conversionToView [ OK ] MultiDimArrayTest.conversionToView (0 ms) [ RUN ] MultiDimArrayTest.conversionToConstView [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) [ RUN ] MultiDimArrayTest.viewBegin [ OK ] MultiDimArrayTest.viewBegin (0 ms) [ RUN ] MultiDimArrayTest.viewEnd [ OK ] MultiDimArrayTest.viewEnd (0 ms) [ RUN ] MultiDimArrayTest.constViewConstBegin [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) [ RUN ] MultiDimArrayTest.constViewConstEnd [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) [----------] 25 tests from MultiDimArrayTest (0 ms total) [----------] 4 tests from MultiDimArrayToMdSpanTest [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) [----------] 9 tests from NelderMeadSimplexTest [ RUN ] NelderMeadSimplexTest.BestVertex [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) [ RUN ] NelderMeadSimplexTest.WorstVertex [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) [ RUN ] NelderMeadSimplexTest.SecondWorstValue [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) [ RUN ] NelderMeadSimplexTest.ReflectionPoint [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) [ RUN ] NelderMeadSimplexTest.SwapOutWorst [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) [ RUN ] NelderMeadSimplexTest.OrientedLength [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) [----------] 9 tests from NelderMeadSimplexTest (0 ms total) [----------] 2 tests from NelderMead [ RUN ] NelderMead.Optimizes2DFunctionCorrectly [ OK ] NelderMead.Optimizes2DFunctionCorrectly (12 ms) [ RUN ] NelderMead.Optimizes3DFunctorCorrectly [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) [----------] 2 tests from NelderMead (12 ms total) [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/0.ResizeWorks [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/0.ReserveWorks [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/0.MoveConstructorWorks [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/0.CanCopyAssign [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/0.CanMoveAssign [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/0.CanSwap [ OK ] PaddedVectorTest/0.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/0 (0 ms total) [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/1.ResizeWorks [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/1.ReserveWorks [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/1.MoveConstructorWorks [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/1.CanCopyAssign [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/1.CanMoveAssign [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/1.CanSwap [ OK ] PaddedVectorTest/1.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/1 (0 ms total) [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/2.ResizeWorks [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/2.ReserveWorks [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/2.MoveConstructorWorks [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/2.CanCopyAssign [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/2.CanMoveAssign [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/2.CanSwap [ OK ] PaddedVectorTest/2.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/2 (0 ms total) [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/3.ResizeWorks [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/3.ReserveWorks [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/3.MoveConstructorWorks [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/3.CanCopyAssign [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/3.CanMoveAssign [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/3.CanSwap [ OK ] PaddedVectorTest/3.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/3 (0 ms total) [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/4.ResizeWorks [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/4.ReserveWorks [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/4.MoveConstructorWorks [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/4.CanCopyAssign [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/4.CanMoveAssign [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/4.CanSwap [ OK ] PaddedVectorTest/4.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/4 (0 ms total) [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/5.ResizeWorks [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/5.ReserveWorks [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/5.MoveConstructorWorks [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/5.CanCopyAssign [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/5.CanMoveAssign [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/5.CanSwap [ OK ] PaddedVectorTest/5.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/5 (0 ms total) [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/6.ResizeWorks [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/6.ReserveWorks [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/6.MoveConstructorWorks [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/6.CanCopyAssign [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/6.CanMoveAssign [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/6.CanSwap [ OK ] PaddedVectorTest/6.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/6 (0 ms total) [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/7.ResizeWorks [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/7.ReserveWorks [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/7.MoveConstructorWorks [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/7.CanCopyAssign [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/7.CanMoveAssign [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/7.CanSwap [ OK ] PaddedVectorTest/7.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/7 (0 ms total) [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/8.ResizeWorks [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/8.ReserveWorks [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/8.MoveConstructorWorks [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/8.CanCopyAssign [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/8.CanMoveAssign [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/8.CanSwap [ OK ] PaddedVectorTest/8.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/8 (0 ms total) [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/9.ResizeWorks [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) [ RUN ] PaddedVectorTest/9.ReserveWorks [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) [ RUN ] PaddedVectorTest/9.MoveConstructorWorks [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) [ RUN ] PaddedVectorTest/9.CanCopyAssign [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) [ RUN ] PaddedVectorTest/9.CanMoveAssign [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) [ RUN ] PaddedVectorTest/9.CanSwap [ OK ] PaddedVectorTest/9.CanSwap (0 ms) [----------] 11 tests from PaddedVectorTest/9 (0 ms total) [----------] 39 tests from RVecTest [ RUN ] RVecTest.CanBeStoredInVector [ OK ] RVecTest.CanBeStoredInVector (0 ms) [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) [ RUN ] RVecTest.WorksAsMutable_rvec [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) [ RUN ] RVecTest.WorksAs_rvec_Array [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) [ RUN ] RVecTest.ComparesEqual [ OK ] RVecTest.ComparesEqual (0 ms) [ RUN ] RVecTest.ComparesUnequal [ OK ] RVecTest.ComparesUnequal (0 ms) [ RUN ] RVecTest.CanAddRVecToRvec [ OK ] RVecTest.CanAddRVecToRvec (0 ms) [ RUN ] RVecTest.CanAddAssignRVecToRvec [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) [ RUN ] RVecTest.CanSubtractRVecFromRvec [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) [ RUN ] RVecTest.CanDotProductRVecByRvec [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) [ RUN ] RVecTest.CanCrossProductRVecByRvec [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) [ RUN ] RVecTest.CanDivideRVecInplace [ OK ] RVecTest.CanDivideRVecInplace (0 ms) [ RUN ] RVecTest.CanScaleRVec [ OK ] RVecTest.CanScaleRVec (0 ms) [ RUN ] RVecTest.CanDivideRVec [ OK ] RVecTest.CanDivideRVec (0 ms) [ RUN ] RVecTest.CanDoUnitvFromRVec [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) [ RUN ] RVecTest.CanSqLengthOfRVec [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) [ RUN ] RVecTest.CanLengthOfRVec [ OK ] RVecTest.CanLengthOfRVec (0 ms) [ RUN ] RVecTest.CanCastToRVec [ OK ] RVecTest.CanCastToRVec (0 ms) [ RUN ] RVecTest.CanCastToDVec [ OK ] RVecTest.CanCastToDVec (0 ms) [ RUN ] RVecTest.CanLeftScalarMultiply [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) [ RUN ] RVecTest.CanRightScalarMultiply [ OK ] RVecTest.CanRightScalarMultiply (0 ms) [ RUN ] RVecTest.CanGetUnitvFromRVec [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) [ RUN ] RVecTest.CanGetSqLengthOfRVec [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) [ RUN ] RVecTest.CanGetLengthOfRVec [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) [ RUN ] RVecTest.CanDoCrossProductOfRVec [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) [ RUN ] RVecTest.CanDoDotProductOfRVec [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) [ RUN ] RVecTest.CanScaleByVector [ OK ] RVecTest.CanScaleByVector (0 ms) [ RUN ] RVecTest.asIVec [ OK ] RVecTest.asIVec (0 ms) [ RUN ] RVecTest.elementWiseMin [ OK ] RVecTest.elementWiseMin (0 ms) [ RUN ] RVecTest.elementWiseMax [ OK ] RVecTest.elementWiseMax (0 ms) [ RUN ] RVecTest.WorksAs_dvec_Reference [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) [ RUN ] RVecTest.WorksAs_ivec_Reference [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) [ RUN ] RVecTest.WorksAs_rvec_Reference [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) [ RUN ] RVecTest.CopyConstructorWorks [ OK ] RVecTest.CopyConstructorWorks (0 ms) [ RUN ] RVecTest.CopyAssignmentWorks [ OK ] RVecTest.CopyAssignmentWorks (0 ms) [ RUN ] RVecTest.MoveConstructorWorks [ OK ] RVecTest.MoveConstructorWorks (0 ms) [ RUN ] RVecTest.MoveAssignmentWorks [ OK ] RVecTest.MoveAssignmentWorks (0 ms) [----------] 39 tests from RVecTest (0 ms total) [----------] Global test environment tear-down [==========] 300 tests from 38 test suites ran. (49 ms total) [ PASSED ] 300 tests. Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "MathUnitTests" end time: Feb 22 23:20 EST "MathUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 33/90 Testing: MdrunUtilityUnitTests 33/90 Test: MdrunUtilityUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrunutility-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunUtilityUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/mdrunutility/tests "MdrunUtilityUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 17 tests from 1 test suite. [----------] Global test environment set-up. [----------] 17 tests from ThreadAffinityTest [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread NOTE: Affinity setting failed. [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (18 ms) [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (12 ms) [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (12 ms) [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing NOTE: Affinity setting for 1/2 threads failed. [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (12 ms) [----------] 17 tests from ThreadAffinityTest (56 ms total) [----------] Global test environment tear-down [==========] 17 tests from 1 test suite ran. (56 ms total) [ PASSED ] 17 tests. Test time = 0.73 sec ---------------------------------------------------------- Test Passed. "MdrunUtilityUnitTests" end time: Feb 22 23:20 EST "MdrunUtilityUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 34/90 Testing: MdrunUtilityMpiUnitTests 34/90 Test: MdrunUtilityMpiUnitTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "4" "${WORKDIR}/gromacs-2022/build/bin/mdrunutility-mpi-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/mdrunutility/tests "MdrunUtilityMpiUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 13 tests from 2 test suites. [----------] Global test environment set-up. [----------] 6 tests from ThreadAffinityMultiRankTest [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (0 ms) [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) [----------] 6 tests from ThreadAffinityMultiRankTest (1 ms total) [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (0 ms) [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (0 ms) [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (1 ms total) [----------] Global test environment tear-down [==========] 13 tests from 2 test suites ran. (3 ms total) [ PASSED ] 13 tests. Test time = 1.01 sec ---------------------------------------------------------- Test Passed. "MdrunUtilityMpiUnitTests" end time: Feb 22 23:20 EST "MdrunUtilityMpiUnitTests" time elapsed: 00:00:01 ---------------------------------------------------------- 35/90 Testing: MDSpanTests 35/90 Test: MDSpanTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdspan-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MDSpanTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/mdspan/tests "MDSpanTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 32 tests from 7 test suites. [----------] Global test environment set-up. [----------] 4 tests from BasicAccessorPolicy [ RUN ] BasicAccessorPolicy.Decay [ OK ] BasicAccessorPolicy.Decay (0 ms) [ RUN ] BasicAccessorPolicy.Access [ OK ] BasicAccessorPolicy.Access (0 ms) [ RUN ] BasicAccessorPolicy.Offset [ OK ] BasicAccessorPolicy.Offset (0 ms) [ RUN ] BasicAccessorPolicy.CopyAccessor [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) [----------] 4 tests from BasicAccessorPolicy (0 ms total) [----------] 4 tests from ExtentsTest [ RUN ] ExtentsTest.Construction [ OK ] ExtentsTest.Construction (0 ms) [ RUN ] ExtentsTest.PurelyStatic [ OK ] ExtentsTest.PurelyStatic (0 ms) [ RUN ] ExtentsTest.RankNought [ OK ] ExtentsTest.RankNought (0 ms) [ RUN ] ExtentsTest.Assignment [ OK ] ExtentsTest.Assignment (0 ms) [----------] 4 tests from ExtentsTest (0 ms total) [----------] 8 tests from MdSpanExtension [ RUN ] MdSpanExtension.SlicingAllStatic [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) [ RUN ] MdSpanExtension.SlicingDynamic [ OK ] MdSpanExtension.SlicingDynamic (0 ms) [ RUN ] MdSpanExtension.SlicingAllStatic3D [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) [ RUN ] MdSpanExtension.SlicingEqualsView3D [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) [ RUN ] MdSpanExtension.additionWorks [ OK ] MdSpanExtension.additionWorks (0 ms) [ RUN ] MdSpanExtension.subtractionWorks [ OK ] MdSpanExtension.subtractionWorks (0 ms) [ RUN ] MdSpanExtension.multiplicationWorks [ OK ] MdSpanExtension.multiplicationWorks (0 ms) [ RUN ] MdSpanExtension.divisionWorks [ OK ] MdSpanExtension.divisionWorks (0 ms) [----------] 8 tests from MdSpanExtension (0 ms total) [----------] 3 tests from LayoutTests [ RUN ] LayoutTests.LayoutRightConstruction [ OK ] LayoutTests.LayoutRightConstruction (0 ms) [ RUN ] LayoutTests.LayoutRightProperties [ OK ] LayoutTests.LayoutRightProperties (0 ms) [ RUN ] LayoutTests.LayoutRightOperator [ OK ] LayoutTests.LayoutRightOperator (0 ms) [----------] 3 tests from LayoutTests (0 ms total) [----------] 1 test from MdSpanTest [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) [----------] 1 test from MdSpanTest (0 ms total) [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > [ RUN ] MdSpanTest/0.Rank [ OK ] MdSpanTest/0.Rank (0 ms) [ RUN ] MdSpanTest/0.DynamicRank [ OK ] MdSpanTest/0.DynamicRank (0 ms) [ RUN ] MdSpanTest/0.Extents [ OK ] MdSpanTest/0.Extents (0 ms) [ RUN ] MdSpanTest/0.Strides [ OK ] MdSpanTest/0.Strides (0 ms) [ RUN ] MdSpanTest/0.Properties [ OK ] MdSpanTest/0.Properties (0 ms) [ RUN ] MdSpanTest/0.Operator [ OK ] MdSpanTest/0.Operator (0 ms) [----------] 6 tests from MdSpanTest/0 (0 ms total) [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > [ RUN ] MdSpanTest/1.Rank [ OK ] MdSpanTest/1.Rank (0 ms) [ RUN ] MdSpanTest/1.DynamicRank [ OK ] MdSpanTest/1.DynamicRank (0 ms) [ RUN ] MdSpanTest/1.Extents [ OK ] MdSpanTest/1.Extents (0 ms) [ RUN ] MdSpanTest/1.Strides [ OK ] MdSpanTest/1.Strides (0 ms) [ RUN ] MdSpanTest/1.Properties [ OK ] MdSpanTest/1.Properties (0 ms) [ RUN ] MdSpanTest/1.Operator [ OK ] MdSpanTest/1.Operator (0 ms) [----------] 6 tests from MdSpanTest/1 (0 ms total) [----------] Global test environment tear-down [==========] 32 tests from 7 test suites ran. (0 ms total) [ PASSED ] 32 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "MDSpanTests" end time: Feb 22 23:20 EST "MDSpanTests" time elapsed: 00:00:00 ---------------------------------------------------------- 36/90 Testing: MdtypesUnitTest 36/90 Test: MdtypesUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/mdtypes-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdtypesUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/mdtypes/tests "MdtypesUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 93 tests from 6 test suites. [----------] Global test environment set-up. [----------] 4 tests from ObservablesReducerTest [ RUN ] ObservablesReducerTest.CanMoveAssign [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) [ RUN ] ObservablesReducerTest.CanMoveConstruct [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) [----------] 4 tests from ObservablesReducerTest (0 ms total) [----------] 2 tests from CheckpointDataTest [ RUN ] CheckpointDataTest.SingleDataTest [ OK ] CheckpointDataTest.SingleDataTest (11 ms) [ RUN ] CheckpointDataTest.MultiDataTest [ OK ] CheckpointDataTest.MultiDataTest (70 ms) [----------] 2 tests from CheckpointDataTest (82 ms total) [----------] 7 tests from ForceBuffers [ RUN ] ForceBuffers.ConstructsUnpinned [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) [ RUN ] ForceBuffers.ConstructsPinned [ OK ] ForceBuffers.ConstructsPinned (0 ms) [ RUN ] ForceBuffers.ConstructsEmpty [ OK ] ForceBuffers.ConstructsEmpty (0 ms) [ RUN ] ForceBuffers.ResizeWorks [ OK ] ForceBuffers.ResizeWorks (0 ms) [ RUN ] ForceBuffers.PaddingWorks [ OK ] ForceBuffers.PaddingWorks (0 ms) [ RUN ] ForceBuffers.CopyWorks [ OK ] ForceBuffers.CopyWorks (0 ms) [ RUN ] ForceBuffers.CopyDoesNotPin [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) [----------] 7 tests from ForceBuffers (0 ms total) [----------] 5 tests from MultipleTimeStepping [ RUN ] MultipleTimeStepping.ChecksNumLevels [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) [ RUN ] MultipleTimeStepping.SelectsForceGroups [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) [ RUN ] MultipleTimeStepping.ChecksStepFactor [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) [ RUN ] MultipleTimeStepping.ChecksIntegrator [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) [----------] 5 tests from MultipleTimeStepping (0 ms total) [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) [----------] 15 tests from ChecksStepInterval/MtsIntervalTest [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) [----------] Global test environment tear-down [==========] 93 tests from 6 test suites ran. (84 ms total) [ PASSED ] 93 tests. Test time = 0.75 sec ---------------------------------------------------------- Test Passed. "MdtypesUnitTest" end time: Feb 22 23:20 EST "MdtypesUnitTest" time elapsed: 00:00:00 ---------------------------------------------------------- 37/90 Testing: OnlineHelpUnitTests 37/90 Test: OnlineHelpUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/onlinehelp-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/OnlineHelpUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/onlinehelp/tests "OnlineHelpUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 22 tests from 4 test suites. [----------] Global test environment set-up. [----------] 6 tests from TextTableFormatterTest [ RUN ] TextTableFormatterTest.HandlesBasicCase [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms) [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) [ RUN ] TextTableFormatterTest.HandlesIndentation [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) [ RUN ] TextTableFormatterTest.HandlesOverflowingLines [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) [ RUN ] TextTableFormatterTest.HandlesEmptyColumns [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) [----------] 6 tests from TextTableFormatterTest (3 ms total) [----------] 3 tests from HelpManagerTest [ RUN ] HelpManagerTest.HandlesRootTopic [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) [ RUN ] HelpManagerTest.HandlesSubTopics [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) [ RUN ] HelpManagerTest.HandlesInvalidTopics [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) [----------] 3 tests from HelpManagerTest (0 ms total) [----------] 2 tests from HelpTopicFormattingTest [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) [----------] 2 tests from HelpTopicFormattingTest (1 ms total) [----------] 11 tests from HelpWriterContextTest [ RUN ] HelpWriterContextTest.FormatsParagraphs [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) [ RUN ] HelpWriterContextTest.FormatsLiteralText [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) [ RUN ] HelpWriterContextTest.FormatsBulletList [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) [ RUN ] HelpWriterContextTest.FormatsEnumeratedList [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) [ RUN ] HelpWriterContextTest.FormatsSimpleTable [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) [ RUN ] HelpWriterContextTest.FormatsGridTable [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) [ RUN ] HelpWriterContextTest.FormatsTitles [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) [----------] 11 tests from HelpWriterContextTest (6 ms total) [----------] Global test environment tear-down [==========] 22 tests from 4 test suites ran. (12 ms total) [ PASSED ] 22 tests. Test time = 0.68 sec ---------------------------------------------------------- Test Passed. "OnlineHelpUnitTests" end time: Feb 22 23:20 EST "OnlineHelpUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 38/90 Testing: OptionsUnitTests 38/90 Test: OptionsUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/options-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/OptionsUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/options/tests "OptionsUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 111 tests from 18 test suites. [----------] Global test environment set-up. [----------] 5 tests from AbstractOptionStorageTest [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) [ RUN ] AbstractOptionStorageTest.HandlesValueAddition [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) [----------] 5 tests from AbstractOptionStorageTest (0 ms total) [----------] 10 tests from FileNameOptionTest [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) [----------] 10 tests from FileNameOptionTest (0 ms total) [----------] 15 tests from FileNameOptionManagerTest [ RUN ] FileNameOptionManagerTest.AddsMissingExtension [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) [----------] 15 tests from FileNameOptionManagerTest (0 ms total) [----------] 1 test from OptionsTest [ RUN ] OptionsTest.FailsOnNonsafeStorage [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) [----------] 1 test from OptionsTest (0 ms total) [----------] 9 tests from OptionsAssignerTest [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) [ RUN ] OptionsAssignerTest.HandlesMultipleParameter [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) [ RUN ] OptionsAssignerTest.HandlesMissingValue [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) [ RUN ] OptionsAssignerTest.HandlesExtraValue [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) [ RUN ] OptionsAssignerTest.HandlesGroups [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) [ RUN ] OptionsAssignerTest.HandlesSections [ OK ] OptionsAssignerTest.HandlesSections (0 ms) [ RUN ] OptionsAssignerTest.HandlesMultipleSources [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) [----------] 9 tests from OptionsAssignerTest (0 ms total) [----------] 4 tests from OptionsAssignerBooleanTest [ RUN ] OptionsAssignerBooleanTest.StoresYesValue [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) [----------] 13 tests from OptionsAssignerIntegerTest [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) [ RUN ] OptionsAssignerIntegerTest.StoresToVector [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesVectors [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) [----------] 5 tests from OptionsAssignerDoubleTest [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) [----------] 9 tests from OptionsAssignerStringTest [ RUN ] OptionsAssignerStringTest.StoresSingleValue [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumValue [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) [ RUN ] OptionsAssignerStringTest.CompletesEnumValue [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) [----------] 9 tests from OptionsAssignerStringTest (0 ms total) [----------] 6 tests from OptionsAssignerEnumTest [ RUN ] OptionsAssignerEnumTest.StoresSingleValue [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) [ RUN ] OptionsAssignerEnumTest.StoresVectorValues [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) [----------] 8 tests from RepeatingOptionSectionTest [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) [----------] 1 test from TimeUnitManagerTest [ RUN ] TimeUnitManagerTest.BasicOperations [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) [----------] 1 test from TimeUnitManagerTest (0 ms total) [----------] 4 tests from TimeUnitBehaviorTest [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) [----------] 2 tests from TreeValueSupportAssignTest [ RUN ] TreeValueSupportAssignTest.AssignsFromTree [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) [----------] 1 test from TreeValueSupportAssignErrorTest [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) [----------] 5 tests from TreeValueSupportCheckTest [ RUN ] TreeValueSupportCheckTest.HandlesEmpty [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) [----------] 6 tests from TreeValueSupportAdjustTest [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) [ RUN ] TreeValueSupportAdjustTest.NormalizesValues [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) [ RUN ] TreeValueSupportAdjustTest.OrdersValues [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total) [----------] 7 tests from TreeValueSupportTest [ RUN ] TreeValueSupportTest.SupportsBooleanOption [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) [ RUN ] TreeValueSupportTest.SupportsIntegerOption [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) [ RUN ] TreeValueSupportTest.SupportsInt64Option [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) [ RUN ] TreeValueSupportTest.SupportsStringOption [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) [ RUN ] TreeValueSupportTest.SupportsFloatOption [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) [ RUN ] TreeValueSupportTest.SupportsDoubleOption [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) [ RUN ] TreeValueSupportTest.SupportsEnumOption [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) [----------] 7 tests from TreeValueSupportTest (4 ms total) [----------] Global test environment tear-down [==========] 111 tests from 18 test suites ran. (10 ms total) [ PASSED ] 111 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "OptionsUnitTests" end time: Feb 22 23:20 EST "OptionsUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 39/90 Testing: PbcutilUnitTest 39/90 Test: PbcutilUnitTest Command: "${WORKDIR}/gromacs-2022/build/bin/pbcutil-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/PbcutilUnitTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/pbcutil/tests "PbcutilUnitTest" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 33 tests from 5 test suites. [----------] Global test environment set-up. [----------] 1 test from ShiftTest [ RUN ] ShiftTest.CoordinateShiftWorks [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) [----------] 1 test from ShiftTest (0 ms total) [----------] 2 tests from MShift [ RUN ] MShift.shiftsAndUnshifts [ OK ] MShift.shiftsAndUnshifts (0 ms) [ RUN ] MShift.shiftsAndUnshiftsSelf [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) [----------] 2 tests from MShift (0 ms total) [----------] 1 test from PbcTest [ RUN ] PbcTest.CalcShiftsWorks [ OK ] PbcTest.CalcShiftsWorks (1 ms) [----------] 1 test from PbcTest (1 ms total) [----------] 2 tests from PbcEnumsTest [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) [----------] 2 tests from PbcEnumsTest (0 ms total) [----------] 27 tests from CorrectCoordinates/COMInPlaceTest [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (17 ms total) [----------] Global test environment tear-down [==========] 33 tests from 5 test suites ran. (18 ms total) [ PASSED ] 33 tests. Test time = 0.68 sec ---------------------------------------------------------- Test Passed. "PbcutilUnitTest" end time: Feb 22 23:20 EST "PbcutilUnitTest" time elapsed: 00:00:00 ---------------------------------------------------------- 40/90 Testing: RandomUnitTests 40/90 Test: RandomUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/random-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/RandomUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/random/tests "RandomUnitTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 44 tests from 10 test suites. [----------] Global test environment set-up. [----------] 4 tests from ExponentialDistributionTest [ RUN ] ExponentialDistributionTest.Output [ OK ] ExponentialDistributionTest.Output (0 ms) [ RUN ] ExponentialDistributionTest.Logical [ OK ] ExponentialDistributionTest.Logical (0 ms) [ RUN ] ExponentialDistributionTest.Reset [ OK ] ExponentialDistributionTest.Reset (0 ms) [ RUN ] ExponentialDistributionTest.AltParam [ OK ] ExponentialDistributionTest.AltParam (0 ms) [----------] 4 tests from ExponentialDistributionTest (0 ms total) [----------] 4 tests from GammaDistributionTest [ RUN ] GammaDistributionTest.Output [ OK ] GammaDistributionTest.Output (0 ms) [ RUN ] GammaDistributionTest.Logical [ OK ] GammaDistributionTest.Logical (0 ms) [ RUN ] GammaDistributionTest.Reset [ OK ] GammaDistributionTest.Reset (0 ms) [ RUN ] GammaDistributionTest.AltParam [ OK ] GammaDistributionTest.AltParam (0 ms) [----------] 4 tests from GammaDistributionTest (0 ms total) [----------] 4 tests from NormalDistributionTest [ RUN ] NormalDistributionTest.Output [ OK ] NormalDistributionTest.Output (0 ms) [ RUN ] NormalDistributionTest.Logical [ OK ] NormalDistributionTest.Logical (0 ms) [ RUN ] NormalDistributionTest.Reset [ OK ] NormalDistributionTest.Reset (0 ms) [ RUN ] NormalDistributionTest.AltParam [ OK ] NormalDistributionTest.AltParam (0 ms) [----------] 4 tests from NormalDistributionTest (0 ms total) [----------] 1 test from SeedTest [ RUN ] SeedTest.makeRandomSeed [ OK ] SeedTest.makeRandomSeed (0 ms) [----------] 1 test from SeedTest (0 ms total) [----------] 6 tests from TabulatedNormalDistributionTest [ RUN ] TabulatedNormalDistributionTest.Output14 [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) [ RUN ] TabulatedNormalDistributionTest.Output16 [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) [ RUN ] TabulatedNormalDistributionTest.Logical [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) [ RUN ] TabulatedNormalDistributionTest.Reset [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) [ RUN ] TabulatedNormalDistributionTest.AltParam [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) [----------] 1 test from TabulatedNormalDistributionTableTest [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) [----------] 6 tests from ThreeFry2x64Test [ RUN ] ThreeFry2x64Test.Logical [ OK ] ThreeFry2x64Test.Logical (0 ms) [ RUN ] ThreeFry2x64Test.InternalCounterSequence [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) [ RUN ] ThreeFry2x64Test.Reseed [ OK ] ThreeFry2x64Test.Reseed (0 ms) [ RUN ] ThreeFry2x64Test.Discard [ OK ] ThreeFry2x64Test.Discard (0 ms) [ RUN ] ThreeFry2x64Test.InvalidCounter [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) [----------] 6 tests from ThreeFry2x64Test (0 ms total) [----------] 4 tests from UniformIntDistributionTest [ RUN ] UniformIntDistributionTest.Output [ OK ] UniformIntDistributionTest.Output (0 ms) [ RUN ] UniformIntDistributionTest.Logical [ OK ] UniformIntDistributionTest.Logical (0 ms) [ RUN ] UniformIntDistributionTest.Reset [ OK ] UniformIntDistributionTest.Reset (0 ms) [ RUN ] UniformIntDistributionTest.AltParam [ OK ] UniformIntDistributionTest.AltParam (0 ms) [----------] 4 tests from UniformIntDistributionTest (0 ms total) [----------] 5 tests from UniformRealDistributionTest [ RUN ] UniformRealDistributionTest.GenerateCanonical [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) [ RUN ] UniformRealDistributionTest.Output [ OK ] UniformRealDistributionTest.Output (0 ms) [ RUN ] UniformRealDistributionTest.Logical [ OK ] UniformRealDistributionTest.Logical (0 ms) [ RUN ] UniformRealDistributionTest.Reset [ OK ] UniformRealDistributionTest.Reset (0 ms) [ RUN ] UniformRealDistributionTest.AltParam [ OK ] UniformRealDistributionTest.AltParam (0 ms) [----------] 5 tests from UniformRealDistributionTest (1 ms total) [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (5 ms total) [----------] Global test environment tear-down [==========] 44 tests from 10 test suites ran. (12 ms total) [ PASSED ] 44 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "RandomUnitTests" end time: Feb 22 23:20 EST "RandomUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 41/90 Testing: RestraintTests 41/90 Test: RestraintTests Command: "${WORKDIR}/gromacs-2022/build/bin/restraintpotential-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/RestraintTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/restraint/tests "RestraintTests" start time: Feb 22 23:20 EST Output: ---------------------------------------------------------- [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from RestraintManager [ RUN ] RestraintManager.restraintList [ OK ] RestraintManager.restraintList (0 ms) [----------] 1 test from RestraintManager (0 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (0 ms total) [ PASSED ] 1 test. Test time = 0.68 sec ---------------------------------------------------------- Test Passed. "RestraintTests" end time: Feb 22 23:21 EST "RestraintTests" time elapsed: 00:00:00 ---------------------------------------------------------- 42/90 Testing: TableUnitTests 42/90 Test: TableUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/table-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TableUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/tables/tests "TableUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 20 tests from 2 test suites. [----------] Global test environment set-up. [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable [ RUN ] SplineTableTest/0.HandlesIncorrectInput [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) [ RUN ] SplineTableTest/0.Sinc [ OK ] SplineTableTest/0.Sinc (0 ms) [ RUN ] SplineTableTest/0.LJ12 [ OK ] SplineTableTest/0.LJ12 (8 ms) [ RUN ] SplineTableTest/0.PmeCorrection [ OK ] SplineTableTest/0.PmeCorrection (0 ms) [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) [ RUN ] SplineTableTest/0.NumericalInputPmeCorr [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) [ RUN ] SplineTableTest/0.TwoFunctions [ OK ] SplineTableTest/0.TwoFunctions (16 ms) [ RUN ] SplineTableTest/0.ThreeFunctions [ OK ] SplineTableTest/0.ThreeFunctions (16 ms) [ RUN ] SplineTableTest/0.Simd [ OK ] SplineTableTest/0.Simd (4 ms) [ RUN ] SplineTableTest/0.SimdTwoFunctions [ OK ] SplineTableTest/0.SimdTwoFunctions (16 ms) [----------] 10 tests from SplineTableTest/0 (64 ms total) [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable [ RUN ] SplineTableTest/1.HandlesIncorrectInput [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) [ RUN ] SplineTableTest/1.Sinc [ OK ] SplineTableTest/1.Sinc (0 ms) [ RUN ] SplineTableTest/1.LJ12 [ OK ] SplineTableTest/1.LJ12 (1 ms) [ RUN ] SplineTableTest/1.PmeCorrection [ OK ] SplineTableTest/1.PmeCorrection (0 ms) [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) [ RUN ] SplineTableTest/1.NumericalInputPmeCorr [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) [ RUN ] SplineTableTest/1.TwoFunctions [ OK ] SplineTableTest/1.TwoFunctions (2 ms) [ RUN ] SplineTableTest/1.ThreeFunctions [ OK ] SplineTableTest/1.ThreeFunctions (2 ms) [ RUN ] SplineTableTest/1.Simd [ OK ] SplineTableTest/1.Simd (0 ms) [ RUN ] SplineTableTest/1.SimdTwoFunctions [ OK ] SplineTableTest/1.SimdTwoFunctions (2 ms) [----------] 10 tests from SplineTableTest/1 (12 ms total) [----------] Global test environment tear-down [==========] 20 tests from 2 test suites ran. (76 ms total) [ PASSED ] 20 tests. Test time = 0.74 sec ---------------------------------------------------------- Test Passed. "TableUnitTests" end time: Feb 22 23:21 EST "TableUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 43/90 Testing: TaskAssignmentUnitTests 43/90 Test: TaskAssignmentUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/taskassignment-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TaskAssignmentUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/taskassignment/tests "TaskAssignmentUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 3 tests from 2 test suites. [----------] Global test environment set-up. [----------] 2 tests from UserTaskAssignmentStringHandlingTest [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) [----------] 1 test from GpuIdAndAssignmentStringHandlingTest [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) [----------] Global test environment tear-down [==========] 3 tests from 2 test suites ran. (0 ms total) [ PASSED ] 3 tests. Test time = 0.67 sec ---------------------------------------------------------- Test Passed. "TaskAssignmentUnitTests" end time: Feb 22 23:21 EST "TaskAssignmentUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 44/90 Testing: GmxTimingTests 44/90 Test: GmxTimingTests Command: "${WORKDIR}/gromacs-2022/build/bin/timing-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxTimingTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/timing/tests "GmxTimingTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 6 tests from 1 test suite. [----------] Global test environment set-up. [----------] 6 tests from TimingTest [ RUN ] TimingTest.ElementCountingWorks [ OK ] TimingTest.ElementCountingWorks (0 ms) [ RUN ] TimingTest.ElementNoCountingWorks [ OK ] TimingTest.ElementNoCountingWorks (0 ms) [ RUN ] TimingTest.SubElementCountingWorks [ OK ] TimingTest.SubElementCountingWorks (0 ms) [ RUN ] TimingTest.SubElementNoCountingWorks [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) [ RUN ] TimingTest.RunWallCycle [ OK ] TimingTest.RunWallCycle (1 ms) [ RUN ] TimingTest.RunWallCycleSub [ OK ] TimingTest.RunWallCycleSub (0 ms) [----------] 6 tests from TimingTest (1 ms total) [----------] Global test environment tear-down [==========] 6 tests from 1 test suite ran. (1 ms total) [ PASSED ] 6 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "GmxTimingTests" end time: Feb 22 23:21 EST "GmxTimingTests" time elapsed: 00:00:00 ---------------------------------------------------------- 45/90 Testing: TopologyTest 45/90 Test: TopologyTest Command: "${WORKDIR}/gromacs-2022/build/bin/topology-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TopologyTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/topology/tests "TopologyTest" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 39 tests from 7 test suites. [----------] Global test environment set-up. [----------] 3 tests from ExclusionBlockTest [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) [ RUN ] ExclusionBlockTest.MergeExclusions [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) [----------] 3 tests from ExclusionBlockTest (0 ms total) [----------] 6 tests from InteractionListTest [ RUN ] InteractionListTest.EmptyWorks [ OK ] InteractionListTest.EmptyWorks (0 ms) [ RUN ] InteractionListTest.CanAddInteractionArray [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) [ RUN ] InteractionListTest.CanAddInteractionPointer [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) [ RUN ] InteractionListTest.CanAddListToOtherList [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) [ RUN ] InteractionListTest.ClearingWorks [ OK ] InteractionListTest.ClearingWorks (0 ms) [----------] 6 tests from InteractionListTest (0 ms total) [----------] 4 tests from MtopTest [ RUN ] MtopTest.RangeBasedLoop [ OK ] MtopTest.RangeBasedLoop (0 ms) [ RUN ] MtopTest.Operators [ OK ] MtopTest.Operators (0 ms) [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) [ RUN ] MtopTest.AtomHasPerturbedChargeIn14Interaction [ OK ] MtopTest.AtomHasPerturbedChargeIn14Interaction (0 ms) [----------] 4 tests from MtopTest (0 ms total) [----------] 2 tests from IListRangeTest [ RUN ] IListRangeTest.RangeBasedLoopWorks [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) [----------] 2 tests from IListRangeTest (0 ms total) [----------] 13 tests from StringTableTest [ RUN ] StringTableTest.AddSingleEntry [ OK ] StringTableTest.AddSingleEntry (2 ms) [ RUN ] StringTableTest.CanAccessWithAt [ OK ] StringTableTest.CanAccessWithAt (1 ms) [ RUN ] StringTableTest.CanAccessWithBracket [ OK ] StringTableTest.CanAccessWithBracket (1 ms) [ RUN ] StringTableTest.ThrowsOutOfRange [ OK ] StringTableTest.ThrowsOutOfRange (2 ms) [ RUN ] StringTableTest.StringCompareIsCorrect [ OK ] StringTableTest.StringCompareIsCorrect (1 ms) [ RUN ] StringTableTest.AddTwoDistinctEntries [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms) [ RUN ] StringTableTest.TryToAddDuplicates [ OK ] StringTableTest.TryToAddDuplicates (1 ms) [ RUN ] StringTableTest.AddLargeNumberOfEntries [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms) [ RUN ] StringTableTest.NoDuplicatesInLargeTable [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms) [ RUN ] StringTableTest.CanWriteToBuffer [ OK ] StringTableTest.CanWriteToBuffer (0 ms) [ RUN ] StringTableTest.Roundtrip [ OK ] StringTableTest.Roundtrip (0 ms) [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) [ RUN ] StringTableTest.CanCopyToLegacyTable [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) [----------] 13 tests from StringTableTest (17 ms total) [----------] 6 tests from LegacySymtabTest [ RUN ] LegacySymtabTest.EmptyOnOpen [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) [ RUN ] LegacySymtabTest.AddSingleEntry [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) [ RUN ] LegacySymtabTest.AddTwoDistinctEntries [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) [ RUN ] LegacySymtabTest.TryToAddDuplicates [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) [----------] 6 tests from LegacySymtabTest (1 ms total) [----------] 5 tests from TopSortTest [ RUN ] TopSortTest.WorksOnEmptyIdef [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) [----------] 5 tests from TopSortTest (0 ms total) [----------] Global test environment tear-down [==========] 39 tests from 7 test suites ran. (20 ms total) [ PASSED ] 39 tests. Test time = 0.69 sec ---------------------------------------------------------- Test Passed. "TopologyTest" end time: Feb 22 23:21 EST "TopologyTest" time elapsed: 00:00:00 ---------------------------------------------------------- 46/90 Testing: PullTest 46/90 Test: PullTest Command: "${WORKDIR}/gromacs-2022/build/bin/pull-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/PullTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/pulling/tests "PullTest" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 8 tests from 1 test suite. [----------] Global test environment set-up. [----------] 8 tests from PullTest [ RUN ] PullTest.MaxPullDistanceXyzScrewBox [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) [ RUN ] PullTest.MaxPullDistanceXyzCubicBox [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) [ RUN ] PullTest.MaxPullDistanceXyzTricBox [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) [ RUN ] PullTest.MaxPullDistanceXyzLongBox [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) [ RUN ] PullTest.MaxPullDistanceXySkewedBox [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) [ RUN ] PullTest.TransformationCoordSimple [ OK ] PullTest.TransformationCoordSimple (0 ms) [ RUN ] PullTest.TransformationCoordAdvanced [ OK ] PullTest.TransformationCoordAdvanced (0 ms) [ RUN ] PullTest.TransformationCoordDummyExpression [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) [----------] 8 tests from PullTest (0 ms total) [----------] Global test environment tear-down [==========] 8 tests from 1 test suite ran. (0 ms total) [ PASSED ] 8 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "PullTest" end time: Feb 22 23:21 EST "PullTest" time elapsed: 00:00:00 ---------------------------------------------------------- 47/90 Testing: SimdUnitTests 47/90 Test: SimdUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/simd-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/SimdUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/simd/tests "SimdUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 288 tests from 22 test suites. [----------] Global test environment set-up. [----------] 9 tests from SimdBootstrapTest [ RUN ] SimdBootstrapTest.loadStore [ OK ] SimdBootstrapTest.loadStore (0 ms) [ RUN ] SimdBootstrapTest.loadU [ OK ] SimdBootstrapTest.loadU (0 ms) [ RUN ] SimdBootstrapTest.storeU [ OK ] SimdBootstrapTest.storeU (0 ms) [ RUN ] SimdBootstrapTest.loadStoreI [ OK ] SimdBootstrapTest.loadStoreI (0 ms) [ RUN ] SimdBootstrapTest.loadUI [ OK ] SimdBootstrapTest.loadUI (0 ms) [ RUN ] SimdBootstrapTest.storeUI [ OK ] SimdBootstrapTest.storeUI (0 ms) [ RUN ] SimdBootstrapTest.simd4LoadStore [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) [ RUN ] SimdBootstrapTest.simd4LoadU [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) [ RUN ] SimdBootstrapTest.simd4StoreU [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) [----------] 9 tests from SimdBootstrapTest (0 ms total) [----------] 41 tests from SimdScalarTest [ RUN ] SimdScalarTest.load [ OK ] SimdScalarTest.load (0 ms) [ RUN ] SimdScalarTest.loadU [ OK ] SimdScalarTest.loadU (0 ms) [ RUN ] SimdScalarTest.store [ OK ] SimdScalarTest.store (0 ms) [ RUN ] SimdScalarTest.storeU [ OK ] SimdScalarTest.storeU (0 ms) [ RUN ] SimdScalarTest.setZero [ OK ] SimdScalarTest.setZero (0 ms) [ RUN ] SimdScalarTest.andNot [ OK ] SimdScalarTest.andNot (0 ms) [ RUN ] SimdScalarTest.fma [ OK ] SimdScalarTest.fma (0 ms) [ RUN ] SimdScalarTest.fms [ OK ] SimdScalarTest.fms (0 ms) [ RUN ] SimdScalarTest.fnma [ OK ] SimdScalarTest.fnma (0 ms) [ RUN ] SimdScalarTest.fnms [ OK ] SimdScalarTest.fnms (0 ms) [ RUN ] SimdScalarTest.maskAdd [ OK ] SimdScalarTest.maskAdd (0 ms) [ RUN ] SimdScalarTest.maskzMul [ OK ] SimdScalarTest.maskzMul (0 ms) [ RUN ] SimdScalarTest.maskzFma [ OK ] SimdScalarTest.maskzFma (0 ms) [ RUN ] SimdScalarTest.abs [ OK ] SimdScalarTest.abs (0 ms) [ RUN ] SimdScalarTest.max [ OK ] SimdScalarTest.max (0 ms) [ RUN ] SimdScalarTest.min [ OK ] SimdScalarTest.min (0 ms) [ RUN ] SimdScalarTest.round [ OK ] SimdScalarTest.round (0 ms) [ RUN ] SimdScalarTest.trunc [ OK ] SimdScalarTest.trunc (0 ms) [ RUN ] SimdScalarTest.reduce [ OK ] SimdScalarTest.reduce (0 ms) [ RUN ] SimdScalarTest.testBits [ OK ] SimdScalarTest.testBits (0 ms) [ RUN ] SimdScalarTest.anyTrue [ OK ] SimdScalarTest.anyTrue (0 ms) [ RUN ] SimdScalarTest.selectByMask [ OK ] SimdScalarTest.selectByMask (0 ms) [ RUN ] SimdScalarTest.selectByNotMask [ OK ] SimdScalarTest.selectByNotMask (0 ms) [ RUN ] SimdScalarTest.blend [ OK ] SimdScalarTest.blend (0 ms) [ RUN ] SimdScalarTest.cvtR2I [ OK ] SimdScalarTest.cvtR2I (0 ms) [ RUN ] SimdScalarTest.cvttR2I [ OK ] SimdScalarTest.cvttR2I (0 ms) [ RUN ] SimdScalarTest.cvtI2R [ OK ] SimdScalarTest.cvtI2R (0 ms) [ RUN ] SimdScalarTest.cvtF2D [ OK ] SimdScalarTest.cvtF2D (0 ms) [ RUN ] SimdScalarTest.cvtD2D [ OK ] SimdScalarTest.cvtD2D (0 ms) [ RUN ] SimdScalarTest.loadI [ OK ] SimdScalarTest.loadI (0 ms) [ RUN ] SimdScalarTest.loadUI [ OK ] SimdScalarTest.loadUI (0 ms) [ RUN ] SimdScalarTest.storeI [ OK ] SimdScalarTest.storeI (0 ms) [ RUN ] SimdScalarTest.storeUI [ OK ] SimdScalarTest.storeUI (0 ms) [ RUN ] SimdScalarTest.andNotI [ OK ] SimdScalarTest.andNotI (0 ms) [ RUN ] SimdScalarTest.testBitsI [ OK ] SimdScalarTest.testBitsI (0 ms) [ RUN ] SimdScalarTest.selectByMaskI [ OK ] SimdScalarTest.selectByMaskI (0 ms) [ RUN ] SimdScalarTest.selectByNotMaskI [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) [ RUN ] SimdScalarTest.blendI [ OK ] SimdScalarTest.blendI (0 ms) [ RUN ] SimdScalarTest.cvtB2IB [ OK ] SimdScalarTest.cvtB2IB (0 ms) [ RUN ] SimdScalarTest.cvtIB2B [ OK ] SimdScalarTest.cvtIB2B (0 ms) [ RUN ] SimdScalarTest.expandScalarsToTriplets [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) [----------] 41 tests from SimdScalarTest (0 ms total) [----------] 8 tests from SimdScalarUtilTest [ RUN ] SimdScalarUtilTest.gatherLoadTranspose [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) [ RUN ] SimdScalarUtilTest.transposeScatterStoreU [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) [ RUN ] SimdScalarUtilTest.transposeScatterIncrU [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) [ RUN ] SimdScalarUtilTest.transposeScatterDecrU [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) [----------] 8 tests from SimdScalarUtilTest (0 ms total) [----------] 37 tests from SimdScalarMathTest [ RUN ] SimdScalarMathTest.copysign [ OK ] SimdScalarMathTest.copysign (0 ms) [ RUN ] SimdScalarMathTest.invsqrtPair [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) [ RUN ] SimdScalarMathTest.inv [ OK ] SimdScalarMathTest.inv (0 ms) [ RUN ] SimdScalarMathTest.maskzInvsqrt [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) [ RUN ] SimdScalarMathTest.log [ OK ] SimdScalarMathTest.log (0 ms) [ RUN ] SimdScalarMathTest.exp2 [ OK ] SimdScalarMathTest.exp2 (0 ms) [ RUN ] SimdScalarMathTest.exp [ OK ] SimdScalarMathTest.exp (0 ms) [ RUN ] SimdScalarMathTest.erf [ OK ] SimdScalarMathTest.erf (0 ms) [ RUN ] SimdScalarMathTest.erfc [ OK ] SimdScalarMathTest.erfc (0 ms) [ RUN ] SimdScalarMathTest.sincos [ OK ] SimdScalarMathTest.sincos (0 ms) [ RUN ] SimdScalarMathTest.sin [ OK ] SimdScalarMathTest.sin (0 ms) [ RUN ] SimdScalarMathTest.cos [ OK ] SimdScalarMathTest.cos (0 ms) [ RUN ] SimdScalarMathTest.tan [ OK ] SimdScalarMathTest.tan (0 ms) [ RUN ] SimdScalarMathTest.asin [ OK ] SimdScalarMathTest.asin (0 ms) [ RUN ] SimdScalarMathTest.acos [ OK ] SimdScalarMathTest.acos (0 ms) [ RUN ] SimdScalarMathTest.atan [ OK ] SimdScalarMathTest.atan (0 ms) [ RUN ] SimdScalarMathTest.atan2 [ OK ] SimdScalarMathTest.atan2 (0 ms) [ RUN ] SimdScalarMathTest.pmeForceCorrection [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) [ RUN ] SimdScalarMathTest.pmePotentialCorrection [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.invSingleAccuracy [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.logSingleAccuracy [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.exp2SingleAccuracy [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.expSingleAccuracy [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.erfSingleAccuracy [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.erfcSingleAccuracy [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.sincosSingleAccuracy [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.sinSingleAccuracy [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.cosSingleAccuracy [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.tanSingleAccuracy [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.asinSingleAccuracy [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.acosSingleAccuracy [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.atanSingleAccuracy [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.atan2SingleAccuracy [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) [----------] 37 tests from SimdScalarMathTest (0 ms total) [----------] 1 test from SimdTest [ RUN ] SimdTest.GmxAligned [ OK ] SimdTest.GmxAligned (0 ms) [----------] 1 test from SimdTest (0 ms total) [----------] 42 tests from SimdFloatingpointTest [ RUN ] SimdFloatingpointTest.setZero [ OK ] SimdFloatingpointTest.setZero (0 ms) [ RUN ] SimdFloatingpointTest.set [ OK ] SimdFloatingpointTest.set (0 ms) [ RUN ] SimdFloatingpointTest.add [ OK ] SimdFloatingpointTest.add (0 ms) [ RUN ] SimdFloatingpointTest.maskAdd [ OK ] SimdFloatingpointTest.maskAdd (0 ms) [ RUN ] SimdFloatingpointTest.sub [ OK ] SimdFloatingpointTest.sub (0 ms) [ RUN ] SimdFloatingpointTest.mul [ OK ] SimdFloatingpointTest.mul (0 ms) [ RUN ] SimdFloatingpointTest.maskzMul [ OK ] SimdFloatingpointTest.maskzMul (0 ms) [ RUN ] SimdFloatingpointTest.fma [ OK ] SimdFloatingpointTest.fma (0 ms) [ RUN ] SimdFloatingpointTest.maskzFma [ OK ] SimdFloatingpointTest.maskzFma (0 ms) [ RUN ] SimdFloatingpointTest.fms [ OK ] SimdFloatingpointTest.fms (0 ms) [ RUN ] SimdFloatingpointTest.fnma [ OK ] SimdFloatingpointTest.fnma (0 ms) [ RUN ] SimdFloatingpointTest.fnms [ OK ] SimdFloatingpointTest.fnms (0 ms) [ RUN ] SimdFloatingpointTest.abs [ OK ] SimdFloatingpointTest.abs (0 ms) [ RUN ] SimdFloatingpointTest.neg [ OK ] SimdFloatingpointTest.neg (0 ms) [ RUN ] SimdFloatingpointTest.and [ OK ] SimdFloatingpointTest.and (0 ms) [ RUN ] SimdFloatingpointTest.or [ OK ] SimdFloatingpointTest.or (0 ms) [ RUN ] SimdFloatingpointTest.xor [ OK ] SimdFloatingpointTest.xor (0 ms) [ RUN ] SimdFloatingpointTest.andNot [ OK ] SimdFloatingpointTest.andNot (0 ms) [ RUN ] SimdFloatingpointTest.max [ OK ] SimdFloatingpointTest.max (0 ms) [ RUN ] SimdFloatingpointTest.min [ OK ] SimdFloatingpointTest.min (0 ms) [ RUN ] SimdFloatingpointTest.round [ OK ] SimdFloatingpointTest.round (0 ms) [ RUN ] SimdFloatingpointTest.roundMode [ OK ] SimdFloatingpointTest.roundMode (0 ms) [ RUN ] SimdFloatingpointTest.trunc [ OK ] SimdFloatingpointTest.trunc (0 ms) [ RUN ] SimdFloatingpointTest.frexp [ OK ] SimdFloatingpointTest.frexp (0 ms) [ RUN ] SimdFloatingpointTest.ldexp [ OK ] SimdFloatingpointTest.ldexp (0 ms) [ RUN ] SimdFloatingpointTest.rsqrt [ OK ] SimdFloatingpointTest.rsqrt (0 ms) [ RUN ] SimdFloatingpointTest.maskzRsqrt [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) [ RUN ] SimdFloatingpointTest.rcp [ OK ] SimdFloatingpointTest.rcp (0 ms) [ RUN ] SimdFloatingpointTest.maskzRcp [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) [ RUN ] SimdFloatingpointTest.selectByNotMask [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) [ RUN ] SimdFloatingpointTest.cmpNe [ OK ] SimdFloatingpointTest.cmpNe (0 ms) [ RUN ] SimdFloatingpointTest.cmpLe [ OK ] SimdFloatingpointTest.cmpLe (0 ms) [ RUN ] SimdFloatingpointTest.cmpLt [ OK ] SimdFloatingpointTest.cmpLt (0 ms) [ RUN ] SimdFloatingpointTest.testBits [ OK ] SimdFloatingpointTest.testBits (0 ms) [ RUN ] SimdFloatingpointTest.andB [ OK ] SimdFloatingpointTest.andB (0 ms) [ RUN ] SimdFloatingpointTest.orB [ OK ] SimdFloatingpointTest.orB (0 ms) [ RUN ] SimdFloatingpointTest.anyTrueB [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) [ RUN ] SimdFloatingpointTest.blend [ OK ] SimdFloatingpointTest.blend (0 ms) [ RUN ] SimdFloatingpointTest.reduce [ OK ] SimdFloatingpointTest.reduce (0 ms) [ RUN ] SimdFloatingpointTest.cvtFloat2Double [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) [ RUN ] SimdFloatingpointTest.cvtDouble2Float [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) [----------] 42 tests from SimdFloatingpointTest (0 ms total) [----------] 16 tests from SimdFloatingpointUtilTest [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) [----------] 23 tests from SimdIntegerTest [ RUN ] SimdIntegerTest.setZero [ OK ] SimdIntegerTest.setZero (0 ms) [ RUN ] SimdIntegerTest.set [ OK ] SimdIntegerTest.set (0 ms) [ RUN ] SimdIntegerTest.add [ OK ] SimdIntegerTest.add (0 ms) [ RUN ] SimdIntegerTest.sub [ OK ] SimdIntegerTest.sub (0 ms) [ RUN ] SimdIntegerTest.mul [ OK ] SimdIntegerTest.mul (0 ms) [ RUN ] SimdIntegerTest.and [ OK ] SimdIntegerTest.and (0 ms) [ RUN ] SimdIntegerTest.andNot [ OK ] SimdIntegerTest.andNot (0 ms) [ RUN ] SimdIntegerTest.or [ OK ] SimdIntegerTest.or (0 ms) [ RUN ] SimdIntegerTest.xor [ OK ] SimdIntegerTest.xor (0 ms) [ RUN ] SimdIntegerTest.extract [ OK ] SimdIntegerTest.extract (0 ms) [ RUN ] SimdIntegerTest.cvtR2I [ OK ] SimdIntegerTest.cvtR2I (0 ms) [ RUN ] SimdIntegerTest.cvttR2I [ OK ] SimdIntegerTest.cvttR2I (0 ms) [ RUN ] SimdIntegerTest.cvtI2R [ OK ] SimdIntegerTest.cvtI2R (0 ms) [ RUN ] SimdIntegerTest.cmpEqAndSelectMask [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) [ RUN ] SimdIntegerTest.cmpLt [ OK ] SimdIntegerTest.cmpLt (0 ms) [ RUN ] SimdIntegerTest.testBits [ OK ] SimdIntegerTest.testBits (0 ms) [ RUN ] SimdIntegerTest.andB [ OK ] SimdIntegerTest.andB (0 ms) [ RUN ] SimdIntegerTest.orB [ OK ] SimdIntegerTest.orB (0 ms) [ RUN ] SimdIntegerTest.anyTrue [ OK ] SimdIntegerTest.anyTrue (0 ms) [ RUN ] SimdIntegerTest.blend [ OK ] SimdIntegerTest.blend (0 ms) [ RUN ] SimdIntegerTest.cvtB2IB [ OK ] SimdIntegerTest.cvtB2IB (0 ms) [ RUN ] SimdIntegerTest.cvtIB2B [ OK ] SimdIntegerTest.cvtIB2B (0 ms) [----------] 23 tests from SimdIntegerTest (0 ms total) [----------] 56 tests from SimdMathTest [ RUN ] SimdMathTest.generateTestPointsFloat [ OK ] SimdMathTest.generateTestPointsFloat (1 ms) [ RUN ] SimdMathTest.copysign [ OK ] SimdMathTest.copysign (0 ms) [ RUN ] SimdMathTest.invsqrt [ OK ] SimdMathTest.invsqrt (0 ms) [ RUN ] SimdMathTest.maskzInvsqrt [ OK ] SimdMathTest.maskzInvsqrt (0 ms) [ RUN ] SimdMathTest.invsqrtPair [ OK ] SimdMathTest.invsqrtPair (0 ms) [ RUN ] SimdMathTest.sqrt [ OK ] SimdMathTest.sqrt (0 ms) [ RUN ] SimdMathTest.sqrtUnsafe [ OK ] SimdMathTest.sqrtUnsafe (0 ms) [ RUN ] SimdMathTest.inv [ OK ] SimdMathTest.inv (0 ms) [ RUN ] SimdMathTest.maskzInv [ OK ] SimdMathTest.maskzInv (0 ms) [ RUN ] SimdMathTest.cbrt [ OK ] SimdMathTest.cbrt (0 ms) [ RUN ] SimdMathTest.invcbrt [ OK ] SimdMathTest.invcbrt (0 ms) [ RUN ] SimdMathTest.log2 [ OK ] SimdMathTest.log2 (0 ms) [ RUN ] SimdMathTest.log [ OK ] SimdMathTest.log (0 ms) [ RUN ] SimdMathTest.exp2 [ OK ] SimdMathTest.exp2 (0 ms) [ RUN ] SimdMathTest.exp2Unsafe [ OK ] SimdMathTest.exp2Unsafe (0 ms) [ RUN ] SimdMathTest.exp [ OK ] SimdMathTest.exp (0 ms) [ RUN ] SimdMathTest.expUnsafe [ OK ] SimdMathTest.expUnsafe (0 ms) [ RUN ] SimdMathTest.pow [ OK ] SimdMathTest.pow (0 ms) [ RUN ] SimdMathTest.powUnsafe [ OK ] SimdMathTest.powUnsafe (0 ms) [ RUN ] SimdMathTest.erf [ OK ] SimdMathTest.erf (0 ms) [ RUN ] SimdMathTest.erfc [ OK ] SimdMathTest.erfc (0 ms) [ RUN ] SimdMathTest.sin [ OK ] SimdMathTest.sin (0 ms) [ RUN ] SimdMathTest.cos [ OK ] SimdMathTest.cos (0 ms) [ RUN ] SimdMathTest.tan [ OK ] SimdMathTest.tan (0 ms) [ RUN ] SimdMathTest.asin [ OK ] SimdMathTest.asin (0 ms) [ RUN ] SimdMathTest.acos [ OK ] SimdMathTest.acos (0 ms) [ RUN ] SimdMathTest.atan [ OK ] SimdMathTest.atan (0 ms) [ RUN ] SimdMathTest.atan2 [ OK ] SimdMathTest.atan2 (0 ms) [ RUN ] SimdMathTest.pmeForceCorrection [ OK ] SimdMathTest.pmeForceCorrection (0 ms) [ RUN ] SimdMathTest.pmePotentialCorrection [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) [ RUN ] SimdMathTest.invsqrtSingleAccuracy [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) [ RUN ] SimdMathTest.sqrtSingleAccuracy [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) [ RUN ] SimdMathTest.invSingleAccuracy [ OK ] SimdMathTest.invSingleAccuracy (0 ms) [ RUN ] SimdMathTest.cbrtSingleAccuracy [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) [ RUN ] SimdMathTest.invcbrtSingleAccuracy [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) [ RUN ] SimdMathTest.log2SingleAccuracy [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) [ RUN ] SimdMathTest.logSingleAccuracy [ OK ] SimdMathTest.logSingleAccuracy (0 ms) [ RUN ] SimdMathTest.exp2SingleAccuracy [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) [ RUN ] SimdMathTest.expSingleAccuracy [ OK ] SimdMathTest.expSingleAccuracy (0 ms) [ RUN ] SimdMathTest.expSingleAccuracyUnsafe [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) [ RUN ] SimdMathTest.powSingleAccuracy [ OK ] SimdMathTest.powSingleAccuracy (0 ms) [ RUN ] SimdMathTest.powSingleAccuracyUnsafe [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) [ RUN ] SimdMathTest.erfSingleAccuracy [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) [ RUN ] SimdMathTest.erfcSingleAccuracy [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) [ RUN ] SimdMathTest.sinSingleAccuracy [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) [ RUN ] SimdMathTest.cosSingleAccuracy [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) [ RUN ] SimdMathTest.tanSingleAccuracy [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) [ RUN ] SimdMathTest.asinSingleAccuracy [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) [ RUN ] SimdMathTest.acosSingleAccuracy [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) [ RUN ] SimdMathTest.atanSingleAccuracy [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) [ RUN ] SimdMathTest.atan2SingleAccuracy [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) [----------] 56 tests from SimdMathTest (15 ms total) [----------] 1 test from EmptyArrayRefTest [ RUN ] EmptyArrayRefTest.IsEmpty [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) [----------] 1 test from EmptyArrayRefTest (0 ms total) [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) [----------] 3 tests from ArrayRefTest/0 (0 ms total) [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) [----------] 3 tests from ArrayRefTest/1 (0 ms total) [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) [----------] 3 tests from ArrayRefTest/2 (0 ms total) [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) [----------] 3 tests from ArrayRefTest/3 (0 ms total) [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefReadWriteTest/0.Assignment [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefReadWriteTest/1.Assignment [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefArithmeticTest/0.Basic [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef [ RUN ] ArrayRefArithmeticTest/1.Basic [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) [----------] 3 tests from SimdVectorOperationsTest [ RUN ] SimdVectorOperationsTest.iprod [ OK ] SimdVectorOperationsTest.iprod (0 ms) [ RUN ] SimdVectorOperationsTest.norm2 [ OK ] SimdVectorOperationsTest.norm2 (0 ms) [ RUN ] SimdVectorOperationsTest.cprod [ OK ] SimdVectorOperationsTest.cprod (0 ms) [----------] 3 tests from SimdVectorOperationsTest (0 ms total) [----------] 32 tests from Simd4FloatingpointTest [ RUN ] Simd4FloatingpointTest.setZero [ OK ] Simd4FloatingpointTest.setZero (0 ms) [ RUN ] Simd4FloatingpointTest.set [ OK ] Simd4FloatingpointTest.set (0 ms) [ RUN ] Simd4FloatingpointTest.add [ OK ] Simd4FloatingpointTest.add (0 ms) [ RUN ] Simd4FloatingpointTest.sub [ OK ] Simd4FloatingpointTest.sub (0 ms) [ RUN ] Simd4FloatingpointTest.mul [ OK ] Simd4FloatingpointTest.mul (0 ms) [ RUN ] Simd4FloatingpointTest.fma [ OK ] Simd4FloatingpointTest.fma (0 ms) [ RUN ] Simd4FloatingpointTest.fms [ OK ] Simd4FloatingpointTest.fms (0 ms) [ RUN ] Simd4FloatingpointTest.fnma [ OK ] Simd4FloatingpointTest.fnma (0 ms) [ RUN ] Simd4FloatingpointTest.fnms [ OK ] Simd4FloatingpointTest.fnms (0 ms) [ RUN ] Simd4FloatingpointTest.abs [ OK ] Simd4FloatingpointTest.abs (0 ms) [ RUN ] Simd4FloatingpointTest.neg [ OK ] Simd4FloatingpointTest.neg (0 ms) [ RUN ] Simd4FloatingpointTest.and [ OK ] Simd4FloatingpointTest.and (0 ms) [ RUN ] Simd4FloatingpointTest.or [ OK ] Simd4FloatingpointTest.or (0 ms) [ RUN ] Simd4FloatingpointTest.xor [ OK ] Simd4FloatingpointTest.xor (0 ms) [ RUN ] Simd4FloatingpointTest.andNot [ OK ] Simd4FloatingpointTest.andNot (0 ms) [ RUN ] Simd4FloatingpointTest.max [ OK ] Simd4FloatingpointTest.max (0 ms) [ RUN ] Simd4FloatingpointTest.min [ OK ] Simd4FloatingpointTest.min (0 ms) [ RUN ] Simd4FloatingpointTest.round [ OK ] Simd4FloatingpointTest.round (0 ms) [ RUN ] Simd4FloatingpointTest.trunc [ OK ] Simd4FloatingpointTest.trunc (0 ms) [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) [ RUN ] Simd4FloatingpointTest.selectByNotMask [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) [ RUN ] Simd4FloatingpointTest.cmpNe [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) [ RUN ] Simd4FloatingpointTest.cmpLe [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) [ RUN ] Simd4FloatingpointTest.cmpLt [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) [ RUN ] Simd4FloatingpointTest.andB [ OK ] Simd4FloatingpointTest.andB (0 ms) [ RUN ] Simd4FloatingpointTest.orB [ OK ] Simd4FloatingpointTest.orB (0 ms) [ RUN ] Simd4FloatingpointTest.anyTrue [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) [ RUN ] Simd4FloatingpointTest.blend [ OK ] Simd4FloatingpointTest.blend (0 ms) [ RUN ] Simd4FloatingpointTest.reduce [ OK ] Simd4FloatingpointTest.reduce (0 ms) [ RUN ] Simd4FloatingpointTest.dotProduct [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) [ RUN ] Simd4FloatingpointTest.transpose [ OK ] Simd4FloatingpointTest.transpose (0 ms) [----------] 32 tests from Simd4FloatingpointTest (0 ms total) [----------] 2 tests from Simd4MathTest [ RUN ] Simd4MathTest.invsqrt [ OK ] Simd4MathTest.invsqrt (0 ms) [ RUN ] Simd4MathTest.invsqrtSingleAccuracy [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) [----------] 2 tests from Simd4MathTest (0 ms total) [----------] 1 test from Simd4VectorOperationsTest [ RUN ] Simd4VectorOperationsTest.norm2 [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) [----------] 1 test from Simd4VectorOperationsTest (0 ms total) [----------] Global test environment tear-down [==========] 288 tests from 22 test suites ran. (17 ms total) [ PASSED ] 288 tests. Test time = 0.69 sec ---------------------------------------------------------- Test Passed. "SimdUnitTests" end time: Feb 22 23:21 EST "SimdUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 48/90 Testing: CompatibilityHelpersTests 48/90 Test: CompatibilityHelpersTests Command: "${WORKDIR}/gromacs-2022/build/bin/compat-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/CompatibilityHelpersTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/compat/tests "CompatibilityHelpersTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 9 tests from 6 test suites. [----------] Global test environment set-up. [----------] 4 tests from TemplateMPTest [ RUN ] TemplateMPTest.MpWithIndexInt [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) [ RUN ] TemplateMPTest.MpWithIndexIntBad [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) [ RUN ] TemplateMPTest.MpWithIndexBool [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) [ RUN ] TemplateMPTest.MpWithIndexEnum [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) [----------] 4 tests from TemplateMPTest (0 ms total) [----------] 1 test from NotNullConstruction [ RUN ] NotNullConstruction.Works [ OK ] NotNullConstruction.Works (0 ms) [----------] 1 test from NotNullConstruction (0 ms total) [----------] 1 test from NotNullCasting [ RUN ] NotNullCasting.Works [ OK ] NotNullCasting.Works (0 ms) [----------] 1 test from NotNullCasting (0 ms total) [----------] 1 test from NotNullAssignment [ RUN ] NotNullAssignment.Works [ OK ] NotNullAssignment.Works (0 ms) [----------] 1 test from NotNullAssignment (0 ms total) [----------] 1 test from MakeNotNull [ RUN ] MakeNotNull.Works [ OK ] MakeNotNull.Works (0 ms) [----------] 1 test from MakeNotNull (0 ms total) [----------] 1 test from NotNull [ RUN ] NotNull.WorksInContainers [ OK ] NotNull.WorksInContainers (0 ms) [----------] 1 test from NotNull (0 ms total) [----------] Global test environment tear-down [==========] 9 tests from 6 test suites ran. (0 ms total) [ PASSED ] 9 tests. Test time = 0.66 sec ---------------------------------------------------------- Test Passed. "CompatibilityHelpersTests" end time: Feb 22 23:21 EST "CompatibilityHelpersTests" time elapsed: 00:00:00 ---------------------------------------------------------- 49/90 Testing: GmxAnaTest 49/90 Test: GmxAnaTest Command: "${WORKDIR}/gromacs-2022/build/bin/gmxana-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxAnaTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxana/tests "GmxAnaTest" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 22 tests from 4 test suites. [----------] Global test environment set-up. [----------] 5 tests from Entropy [ RUN ] Entropy.Schlitter_300_NoLinear [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) [ RUN ] Entropy.Schlitter_300_Linear [ OK ] Entropy.Schlitter_300_Linear (0 ms) [ RUN ] Entropy.QuasiHarmonic_300_NoLinear [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) [ RUN ] Entropy.QuasiHarmonic_200_NoLinear [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) [ RUN ] Entropy.QuasiHarmonic_200_Linear [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) [----------] 5 tests from Entropy (3 ms total) [----------] 1 test from GmxChiTest [ RUN ] GmxChiTest.gmxchiWorksWithAll 10 residues with dihedrals found 46 dihedrals found Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 j after resetting (nr. active dihedrals) = 46 Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg Now calculating transitions... Total number of transitions: 0 Now printing out transitions and OPs... Now printing out rotamer occupancies... Now calculating Chi product trajectories... Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg gmx chi is deprecated. See https://gitlab.com/gromacs/gromacs/-/issues/4108 if you are interested in preserving it! [ OK ] GmxChiTest.gmxchiWorksWithAll (760 ms) [----------] 1 test from GmxChiTest (813 ms total) [----------] 10 tests from MindistTest [ RUN ] MindistTest.mindistWorksWithSingleAtoms Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 0: 'atom1' Selected 1: 'atom2' [ OK ] MindistTest.mindistWorksWithSingleAtoms (16 ms) [ RUN ] MindistTest.mindistWorksWithMultipleAtoms Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 2: 'atom3' Selected 3: 'atoms12' [ OK ] MindistTest.mindistWorksWithMultipleAtoms (6 ms) [ RUN ] MindistTest.mindistDoesNotPickUpContacts Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 0: 'atom1' Selected 1: 'atom2' [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms) [ RUN ] MindistTest.mindistPicksUpContacts Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 0: 'atom1' Selected 1: 'atom2' [ OK ] MindistTest.mindistPicksUpContacts (6 ms) [ RUN ] MindistTest.ngWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 0: 'atom1' Selected 1: 'atom2' Selected 2: 'atom3' [ OK ] MindistTest.ngWorks (6 ms) [ RUN ] MindistTest.groupWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 3: 'atoms12' Selected 2: 'atom3' [ OK ] MindistTest.groupWorks (7 ms) [ RUN ] MindistTest.maxDistWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 2: 'atom3' Selected 3: 'atoms12' [ OK ] MindistTest.maxDistWorks (5 ms) [ RUN ] MindistTest.noPbcWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 0: 'atom1' Selected 1: 'atom2' [ OK ] MindistTest.noPbcWorks (5 ms) [ RUN ] MindistTest.resPerTimeWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 3: 'atoms12' Selected 2: 'atom3' [ OK ] MindistTest.resPerTimeWorks (9 ms) [ RUN ] MindistTest.matrixWorks Group 0 ( atom1) has 1 elements Group 1 ( atom2) has 1 elements Group 2 ( atom3) has 1 elements Group 3 ( atoms12) has 2 elements Group 4 ( atoms23) has 2 elements Group 5 ( atoms123) has 3 elements Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Selected 5: 'atoms123' Special case: making distance matrix between all atoms in group atoms123 [ OK ] MindistTest.matrixWorks (5 ms) [----------] 10 tests from MindistTest (77 ms total) [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: trr version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (5 ms) [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (5 ms) [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (5 ms) [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (5 ms) [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (5 ms) [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 Group 0 ( System) has 6 elements Group 1 ( Water) has 6 elements Group 2 ( SOL) has 6 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Selected 0: 'System' [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (5 ms) [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (33 ms total) [----------] Global test environment tear-down [==========] 22 tests from 4 test suites ran. (927 ms total) [ PASSED ] 22 tests. Test time = 1.60 sec ---------------------------------------------------------- Test Passed. "GmxAnaTest" end time: Feb 22 23:21 EST "GmxAnaTest" time elapsed: 00:00:01 ---------------------------------------------------------- 50/90 Testing: GmxPreprocessTests 50/90 Test: GmxPreprocessTests Command: "${WORKDIR}/gromacs-2022/build/bin/gmxpreprocess-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/GmxPreprocessTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests "GmxPreprocessTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 79 tests from 11 test suites. [----------] Global test environment set-up. [----------] 4 tests from GenconfTest [ RUN ] GenconfTest.nbox_Works [ OK ] GenconfTest.nbox_Works (4 ms) [ RUN ] GenconfTest.nbox_norenumber_Works [ OK ] GenconfTest.nbox_norenumber_Works (3 ms) [ RUN ] GenconfTest.nbox_dist_Works [ OK ] GenconfTest.nbox_dist_Works (3 ms) [ RUN ] GenconfTest.nbox_rot_Works center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 [ OK ] GenconfTest.nbox_rot_Works (3 ms) [----------] 4 tests from GenconfTest (14 ms total) [----------] 2 tests from GenionTest [ RUN ] GenionTest.HighConcentrationIonPlacement NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 1308.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022 (single precision) Group 0 ( System) has 653 elements Group 1 ( Water) has 648 elements Group 2 ( SOL) has 648 elements Group 3 ( non-Water) has 5 elements Group 4 ( Other) has 5 elements Group 5 ( METH) has 5 elements Select a group: Number of (3-atomic) solvent molecules: 216 Using random seed 1997. Replacing solvent molecule 56 (atom 168) with NA Replacing solvent molecule 120 (atom 360) with NA Replacing solvent molecule 182 (atom 546) with NA Replacing solvent molecule 71 (atom 213) with NA Replacing solvent molecule 189 (atom 567) with CL Replacing solvent molecule 54 (atom 162) with CL Replacing solvent molecule 155 (atom 465) with CL Replacing solvent molecule 99 (atom 297) with CL Setting the LD random seed to 2103442322 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Analysing residue names: There are: 216 Water residues There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data Will try to add 4 NA ions and 4 CL ions. Select a continuous group of solvent molecules Selected 1: 'Water' [ OK ] GenionTest.HighConcentrationIonPlacement (134 ms) [ RUN ] GenionTest.NoIonPlacement NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 1308.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022 (single precision) No ions to add, will just copy input configuration. Setting the LD random seed to -957383842 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Analysing residue names: There are: 216 Water residues There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] GenionTest.NoIonPlacement (126 ms) [----------] 2 tests from GenionTest (260 ms total) [----------] 1 test from GenRestrTest [ RUN ] GenRestrTest.SimpleRestraintsGenerated Reading structure file Group 0 ( System) has 156 elements Group 1 ( Protein) has 156 elements Group 2 ( Protein-H) has 75 elements Group 3 ( C-alpha) has 10 elements Group 4 ( Backbone) has 30 elements Group 5 ( MainChain) has 40 elements Group 6 ( MainChain+Cb) has 49 elements Group 7 ( MainChain+H) has 52 elements Group 8 ( SideChain) has 104 elements Group 9 ( SideChain-H) has 35 elements Select a group: Select group to position restrain Selected 3: 'C-alpha' [ OK ] GenRestrTest.SimpleRestraintsGenerated (5 ms) [----------] 1 test from GenRestrTest (5 ms total) [----------] 9 tests from PreprocessingAtomTypesTest [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) [----------] 10 tests from PreprocessingBondAtomTypeTest [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) [----------] 1 test from GromppDirectiveTest [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames Ignoring obsolete mdp entry 'title' Generating 1-4 interactions: fudge = 0.5 NOTE 1 [file directives.top, line 44]: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: NVE simulation: will use the initial temperature of 300.000 K for determining the Verlet buffer size There were 2 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2022 (single precision) Setting the LD random seed to -285232322 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'A' Setting gen_seed to 2121645055 Velocities were taken from a Maxwell distribution at 300 K Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (9 ms) [----------] 1 test from GromppDirectiveTest (9 ms total) [----------] 5 tests from InsertMoleculesTest [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Added 1 molecules (out of 1 requested) Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro Output configuration contains 8 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (6 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 3 success (now 6 atoms)! Try 4 success (now 8 atoms)! Try 5 success (now 10 atoms)! Added 5 molecules (out of 5 requested) Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro Output configuration contains 10 atoms in 10 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Try 2 success (now 10 atoms)! Added 2 molecules (out of 2 requested) Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro Output configuration contains 10 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (5 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement Reading solute configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 650 atoms)! Try 2 success (now 652 atoms)! Try 3 success (now 654 atoms)! Try 4 success (now 656 atoms)! Added 4 molecules (out of 4 requested) Replaced 8 residues (24 atoms) Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro Output configuration contains 632 atoms in 212 residues [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (8 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Read 4 positions from file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) Try 13 success (now 6 atoms)! Added 3 molecules (out of 4 requested) Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro Output configuration contains 6 atoms in 3 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (6 ms) [----------] 5 tests from InsertMoleculesTest (29 ms total) [----------] 23 tests from GetIrTest [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines Ignoring obsolete mdp entry 'title' Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) [ RUN ] GetIrTest.AcceptsKeyWithoutValue NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsKeyWithoutValue (4 ms) [ RUN ] GetIrTest.RejectsValueWithoutKey [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (4 ms) [ RUN ] GetIrTest.AcceptsEmptyLines NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsEmptyLines (4 ms) [ RUN ] GetIrTest.MtsCheckNstcalcenergy ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.MtsCheckNstcalcenergy (2 ms) [ RUN ] GetIrTest.MtsCheckNstenergy ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (5) NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.MtsCheckNstenergy (2 ms) [ RUN ] GetIrTest.MtsCheckNstpcouple ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: Pressure coupling incorrect number of values (I need exactly 1) ERROR 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: Pressure coupling incorrect number of values (I need exactly 1) ERROR 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: With multiple time stepping, nstpcouple should be a mutiple of mts-factor NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. ERROR 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. ERROR 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: compressibility must be > 0 when using pressure coupling Berendsen [ OK ] GetIrTest.MtsCheckNstpcouple (2 ms) [ RUN ] GetIrTest.MtsCheckNstdhdl ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: Setting nstcalcenergy (100) equal to nstdhdl (5) NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. ERROR 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: Lambda state must be set, either with init-lambda-state or with init-lambda [ OK ] GetIrTest.MtsCheckNstdhdl (2 ms) [ RUN ] GetIrTest.AcceptsElectricField NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsElectricField (4 ms) [ RUN ] GetIrTest.AcceptsElectricFieldPulsed NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsElectricFieldPulsed (4 ms) [ RUN ] GetIrTest.AcceptsElectricFieldOscillating NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsElectricFieldOscillating (4 ms) [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) [ RUN ] GetIrTest.AcceptsImplicitSolventNo NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsImplicitSolventNo (6 ms) [ RUN ] GetIrTest.RejectsImplicitSolventYes [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) [ RUN ] GetIrTest.AcceptsMimic NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsMimic (3 ms) [ RUN ] GetIrTest.AcceptsTransformationCoord NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: pull-coord2 has a non-zero force constant and is also referenced in pull-coord1-expression. Make sure that this is intended. In most use cases, the pull coordinates referenced by a transformation coordinate should have their force constant set to zero. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: pull-coord1 cannot have type 'constraint' and geometry 'transformation' NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (2 ms) [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: pull-coord2 can not use pull-coord1 in the transformation since this is a constraint NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (2 ms) [ RUN ] GetIrTest.InvalidTransformationCoordDxValue ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 'transformation' NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.InvalidTransformationCoordDxValue (2 ms) [ RUN ] GetIrTest.MissingTransformationCoordExpression ERROR 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: pull-coord1-expression not set for pull coordinate of geometry 'transformation' NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) [----------] 23 tests from GetIrTest (59 ms total) [----------] 5 tests from SolvateTest [ RUN ] SolvateTest.cs_box_Works Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 1x1x1 boxes Solvent box contains 270 atoms in 90 residues Removed 129 solvent atoms due to solvent-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 47 residues Generated solvent containing 141 atoms in 47 residues Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro Output configuration contains 141 atoms in 47 residues Volume : 1.331 (nm^3) Density : 1056.36 (g/l) Number of solvent molecules: 47 [ OK ] SolvateTest.cs_box_Works (9 ms) [ RUN ] SolvateTest.cs_cp_Works Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 2x2x2 boxes Solvent box contains 3660 atoms in 1220 residues Removed 987 solvent atoms due to solvent-solvent overlap Removed 15 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 886 residues Generated solvent containing 2658 atoms in 886 residues Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro Output configuration contains 2664 atoms in 888 residues Volume : 27.2709 (nm^3) Density : 974.777 (g/l) Number of solvent molecules: 886 [ OK ] SolvateTest.cs_cp_Works (29 ms) [ RUN ] SolvateTest.cs_cp_p_Works Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 2x2x2 boxes Solvent box contains 3660 atoms in 1220 residues Removed 987 solvent atoms due to solvent-solvent overlap Removed 15 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 886 residues Generated solvent containing 2658 atoms in 886 residues Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro Output configuration contains 2664 atoms in 888 residues Volume : 27.2709 (nm^3) Density : 974.777 (g/l) Number of solvent molecules: 886 Processing topology Adding line for 886 solvent molecules with resname (SOL) to topology file (${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) [ OK ] SolvateTest.cs_cp_p_Works (37 ms) [ RUN ] SolvateTest.shell_Works Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 2x2x2 boxes Solvent box contains 3660 atoms in 1220 residues Removed 987 solvent atoms due to solvent-solvent overlap Removed 1902 solvent atoms more than 1.000000 nm from solute. Removed 15 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 252 residues Generated solvent containing 756 atoms in 252 residues Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro Output configuration contains 762 atoms in 254 residues Volume : 27.2709 (nm^3) Density : 279.3 (g/l) Number of solvent molecules: 252 [ OK ] SolvateTest.shell_Works (16 ms) [ RUN ] SolvateTest.update_Topology_Works Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 3x3x3 boxes Solvent box contains 14952 atoms in 4984 residues Removed 2787 solvent atoms due to solvent-solvent overlap Removed 30 solvent atoms due to solute-solvent overlap Sorting configuration Found 2 different molecule types: HOH ( 3 atoms): 1876 residues SOL ( 3 atoms): 2169 residues Generated solvent containing 0 atoms in 0 residues Writing generated configuration to ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro Output configuration contains 12141 atoms in 4047 residues Volume : 125 (nm^3) Density : 968.963 (g/l) Number of solvent molecules: 4045 Processing topology Adding line for 1876 solvent molecules with resname (HOH) to topology file (${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) Adding line for 2169 solvent molecules with resname (SOL) to topology file (${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) [ OK ] SolvateTest.update_Topology_Works (115 ms) [----------] 5 tests from SolvateTest (207 ms total) [----------] 1 test from TopDirTests [ RUN ] TopDirTests.NamesArrayHasCorrectSize [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) [----------] 1 test from TopDirTests (0 ms total) [----------] 18 tests from SinglePeptideFragments/EditconfTest [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (5 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (4 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (5 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (6 ms) [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 Select a group for output: Group 0 ( two_residues) has 23 elements There is one group in the index Note that major changes are planned in future for editconf, to improve usability and utility. Read 252 atoms Volume: 338.104 nm^3, corresponds to roughly 152100 electrons No velocities found [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (5 ms) [----------] 18 tests from SinglePeptideFragments/EditconfTest (96 ms total) [----------] Global test environment tear-down [==========] 79 tests from 11 test suites ran. (682 ms total) [ PASSED ] 79 tests. Test time = 1.38 sec ---------------------------------------------------------- Test Passed. "GmxPreprocessTests" end time: Feb 22 23:21 EST "GmxPreprocessTests" time elapsed: 00:00:01 ---------------------------------------------------------- 51/90 Testing: Pdb2gmx1Test 51/90 Test: Pdb2gmx1Test Command: "${WORKDIR}/gromacs-2022/build/bin/pdb2gmx1-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/Pdb2gmx1Test.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests "Pdb2gmx1Test" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 30 tests from 1 test suite. [----------] Global test environment set-up. [----------] 30 tests from Oplsaa/Pdb2gmxTest [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 0 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 0 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 0 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 0 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (35 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 0 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (97 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Marked 124 virtual sites Added 16 dummy masses Added 26 new constraints Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 130 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (42 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Marked 132 virtual sites Added 10 dummy masses Added 19 new constraints Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 133 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (43 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Marked 123 virtual sites Added 22 dummy masses Added 35 new constraints Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 132 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Marked 111 virtual sites Added 18 dummy masses Added 31 new constraints Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 116 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Marked 447 virtual sites Added 58 dummy masses Added 101 new constraints Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 462 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (107 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 0 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 0 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 0 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 0 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (38 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 0 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (95 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Marked 124 virtual sites Added 16 dummy masses Added 26 new constraints Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 130 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Marked 132 virtual sites Added 10 dummy masses Added 19 new constraints Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 133 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Marked 123 virtual sites Added 22 dummy masses Added 35 new constraints Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 132 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Marked 111 virtual sites Added 18 dummy masses Added 31 new constraints Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 116 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Marked 447 virtual sites Added 58 dummy masses Added 101 new constraints Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 462 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (118 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 0 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (39 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 0 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (39 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 0 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 0 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (35 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 0 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (96 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Marked 124 virtual sites Added 16 dummy masses Added 26 new constraints Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 663 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 130 virtual sites Total mass 1846.112 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Marked 132 virtual sites Added 10 dummy masses Added 19 new constraints Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 778 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 133 virtual sites Total mass 2088.357 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Marked 123 virtual sites Added 22 dummy masses Added 35 new constraints Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 696 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 132 virtual sites Total mass 1861.128 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Marked 111 virtual sites Added 18 dummy masses Added 31 new constraints Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: PRO-COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 618 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 116 virtual sites Total mass 1662.883 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/oplsaa.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Marked 447 virtual sites Added 58 dummy masses Added 101 new constraints Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Oplsaa) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2524 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 462 virtual sites Total mass 6908.578 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Oplsaa force field and the tip5p water model are used. --------- ETON ESAELP ------------ [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (104 ms) [----------] 30 tests from Oplsaa/Pdb2gmxTest (1566 ms total) [----------] Global test environment tear-down [==========] 30 tests from 1 test suite ran. (1566 ms total) [ PASSED ] 30 tests. Test time = 2.25 sec ---------------------------------------------------------- Test Passed. "Pdb2gmx1Test" end time: Feb 22 23:21 EST "Pdb2gmx1Test" time elapsed: 00:00:02 ---------------------------------------------------------- 52/90 Testing: Pdb2gmx2Test 52/90 Test: Pdb2gmx2Test Command: "${WORKDIR}/gromacs-2022/build/bin/pdb2gmx2-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/Pdb2gmx2Test.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests "Pdb2gmx2Test" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 40 tests from 2 test suites. [----------] Global test environment set-up. [----------] 20 tests from G43a1/Pdb2gmxTest [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 305 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 165 atoms Making bonds... Number of bonds was 172, now 167 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 77 impropers, 241 angles 267 pairs, 167 bonds and 0 virtual sites Total mass 1846.116 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 429 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 202 atoms Making bonds... Number of bonds was 216, now 211 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 134 impropers, 316 angles 273 pairs, 211 bonds and 0 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 349 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 168 atoms Making bonds... Number of bonds was 179, now 174 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 102 impropers, 260 angles 242 pairs, 174 bonds and 0 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 299 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 150 atoms Making bonds... Number of bonds was 159, now 154 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 80 impropers, 227 angles 232 pairs, 154 bonds and 0 virtual sites Total mass 1662.887 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1256 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 635 atoms Making bonds... Number of bonds was 655, now 650 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 350 impropers, 955 angles 972 pairs, 650 bonds and 0 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (68 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 37 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 305 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 165 atoms Making bonds... Number of bonds was 172, now 167 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 77 impropers, 241 angles 267 pairs, 167 bonds and 37 virtual sites Total mass 1846.116 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 53 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 429 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 202 atoms Making bonds... Number of bonds was 216, now 211 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 134 impropers, 316 angles 273 pairs, 211 bonds and 51 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 36 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 349 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 168 atoms Making bonds... Number of bonds was 179, now 174 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 102 impropers, 260 angles 242 pairs, 174 bonds and 36 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 33 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 299 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 150 atoms Making bonds... Number of bonds was 159, now 154 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 80 impropers, 227 angles 232 pairs, 154 bonds and 31 virtual sites Total mass 1662.887 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 146 virtual sites Added 10 dummy masses Added 29 new constraints WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1256 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 635 atoms Making bonds... Number of bonds was 655, now 650 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 350 impropers, 955 angles 972 pairs, 650 bonds and 137 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos43a1 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (70 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 305 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 165 atoms Making bonds... Number of bonds was 172, now 167 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 77 impropers, 241 angles 267 pairs, 167 bonds and 0 virtual sites Total mass 1846.116 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 429 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 202 atoms Making bonds... Number of bonds was 216, now 211 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 134 impropers, 316 angles 273 pairs, 211 bonds and 0 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 349 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 168 atoms Making bonds... Number of bonds was 179, now 174 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 102 impropers, 260 angles 242 pairs, 174 bonds and 0 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (35 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 299 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 150 atoms Making bonds... Number of bonds was 159, now 154 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 80 impropers, 227 angles 232 pairs, 154 bonds and 0 virtual sites Total mass 1662.887 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (35 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1256 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 635 atoms Making bonds... Number of bonds was 655, now 650 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 350 impropers, 955 angles 972 pairs, 650 bonds and 0 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (68 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 37 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 305 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 165 atoms Making bonds... Number of bonds was 172, now 167 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 77 impropers, 241 angles 267 pairs, 167 bonds and 37 virtual sites Total mass 1846.116 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 53 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 429 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 202 atoms Making bonds... Number of bonds was 216, now 211 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 134 impropers, 316 angles 273 pairs, 211 bonds and 51 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 36 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 349 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 168 atoms Making bonds... Number of bonds was 179, now 174 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 102 impropers, 260 angles 242 pairs, 174 bonds and 36 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 33 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 299 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 150 atoms Making bonds... Number of bonds was 159, now 154 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 80 impropers, 227 angles 232 pairs, 154 bonds and 31 virtual sites Total mass 1662.887 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos43a1.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 146 virtual sites Added 10 dummy masses Added 29 new constraints WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1256 dihedrals Using the Gromos43a1 force field in directory gromos43a1.ff going to rename gromos43a1.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos43a1) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 635 atoms Making bonds... Number of bonds was 655, now 650 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 350 impropers, 955 angles 972 pairs, 650 bonds and 137 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos43a1 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (70 ms) [----------] 20 tests from G43a1/Pdb2gmxTest (885 ms total) [----------] 20 tests from G53a6/Pdb2gmxTest [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 312 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 167 atoms Making bonds... Number of bonds was 174, now 169 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 79 impropers, 245 angles 267 pairs, 169 bonds and 0 virtual sites Total mass 1846.116 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (41 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 443 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 206 atoms Making bonds... Number of bonds was 220, now 215 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 138 impropers, 324 angles 273 pairs, 215 bonds and 0 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 356 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 170 atoms Making bonds... Number of bonds was 181, now 176 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 104 impropers, 264 angles 242 pairs, 176 bonds and 0 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 306 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 152 atoms Making bonds... Number of bonds was 161, now 156 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 82 impropers, 231 angles 232 pairs, 156 bonds and 0 virtual sites Total mass 1662.887 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1270 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 639 atoms Making bonds... Number of bonds was 659, now 654 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 354 impropers, 963 angles 972 pairs, 654 bonds and 0 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (69 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 39 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 312 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 167 atoms Making bonds... Number of bonds was 174, now 169 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 79 impropers, 245 angles 267 pairs, 169 bonds and 39 virtual sites Total mass 1846.116 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 57 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 443 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 206 atoms Making bonds... Number of bonds was 220, now 215 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 138 impropers, 324 angles 273 pairs, 215 bonds and 55 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 38 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 356 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 170 atoms Making bonds... Number of bonds was 181, now 176 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 104 impropers, 264 angles 242 pairs, 176 bonds and 38 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 35 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 306 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 152 atoms Making bonds... Number of bonds was 161, now 156 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 82 impropers, 231 angles 232 pairs, 156 bonds and 33 virtual sites Total mass 1662.887 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 150 virtual sites Added 10 dummy masses Added 29 new constraints WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1270 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 639 atoms Making bonds... Number of bonds was 659, now 654 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 354 impropers, 963 angles 972 pairs, 654 bonds and 141 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos53a6 force field and the spc water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (74 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 312 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 167 atoms Making bonds... Number of bonds was 174, now 169 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 79 impropers, 245 angles 267 pairs, 169 bonds and 0 virtual sites Total mass 1846.116 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 443 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 206 atoms Making bonds... Number of bonds was 220, now 215 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 138 impropers, 324 angles 273 pairs, 215 bonds and 0 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 356 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 170 atoms Making bonds... Number of bonds was 181, now 176 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 104 impropers, 264 angles 242 pairs, 176 bonds and 0 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 306 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 152 atoms Making bonds... Number of bonds was 161, now 156 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 82 impropers, 231 angles 232 pairs, 156 bonds and 0 virtual sites Total mass 1662.887 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1270 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 639 atoms Making bonds... Number of bonds was 659, now 654 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 354 impropers, 963 angles 972 pairs, 654 bonds and 0 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (68 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 39 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 267 pairs Before cleaning: 312 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 167 atoms Making bonds... Number of bonds was 174, now 169 Generating angles, dihedrals and pairs... Making cmap torsions... There are 90 dihedrals, 79 impropers, 245 angles 267 pairs, 169 bonds and 39 virtual sites Total mass 1846.116 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 57 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 273 pairs Before cleaning: 443 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 206 atoms Making bonds... Number of bonds was 220, now 215 Generating angles, dihedrals and pairs... Making cmap torsions... There are 93 dihedrals, 138 impropers, 324 angles 273 pairs, 215 bonds and 55 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 38 virtual sites Added 4 dummy masses Added 8 new constraints WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 242 pairs Before cleaning: 356 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 170 atoms Making bonds... Number of bonds was 181, now 176 Generating angles, dihedrals and pairs... Making cmap torsions... There are 81 dihedrals, 104 impropers, 264 angles 242 pairs, 176 bonds and 38 virtual sites Total mass 1861.132 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 35 virtual sites Added 4 dummy masses Added 10 new constraints WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 232 pairs Before cleaning: 306 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 152 atoms Making bonds... Number of bonds was 161, now 156 Generating angles, dihedrals and pairs... Making cmap torsions... There are 78 dihedrals, 82 impropers, 231 angles 232 pairs, 156 bonds and 33 virtual sites Total mass 1662.887 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.rtp Using default: removing proper dihedrals found on the same bond as a proper dihedral Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/gromos53a6.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Marked 150 virtual sites Added 10 dummy masses Added 29 new constraints WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 972 pairs Before cleaning: 1270 dihedrals Using the Gromos53a6 force field in directory gromos53a6.ff going to rename gromos53a6.ff/aminoacids.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Gromos53a6) Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 639 atoms Making bonds... Number of bonds was 659, now 654 Generating angles, dihedrals and pairs... Making cmap torsions... There are 321 dihedrals, 354 impropers, 963 angles 972 pairs, 654 bonds and 141 virtual sites Total mass 6908.582 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Gromos53a6 force field and the spce water model are used. --------- ETON ESAELP ------------ [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (72 ms) [----------] 20 tests from G53a6/Pdb2gmxTest (934 ms total) [----------] Global test environment tear-down [==========] 40 tests from 2 test suites ran. (1819 ms total) [ PASSED ] 40 tests. Test time = 2.51 sec ---------------------------------------------------------- Test Passed. "Pdb2gmx2Test" end time: Feb 22 23:21 EST "Pdb2gmx2Test" time elapsed: 00:00:02 ---------------------------------------------------------- 53/90 Testing: Pdb2gmx3Test 53/90 Test: Pdb2gmx3Test Command: "${WORKDIR}/gromacs-2022/build/bin/pdb2gmx3-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/Pdb2gmx3Test.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/gmxpreprocess/tests "Pdb2gmx3Test" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 39 tests from 6 test suites. [----------] Global test environment set-up. [----------] 10 tests from Amber/Pdb2gmxTest [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Before cleaning: 653 pairs Before cleaning: 691 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 255, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 691 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 0 virtual sites Total mass 1846.132 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (52 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Before cleaning: 748 pairs Before cleaning: 788 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 291, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 788 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 0 virtual sites Total mass 2088.366 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Before cleaning: 676 pairs Before cleaning: 727 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 262, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 727 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 0 virtual sites Total mass 1861.124 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (45 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Before cleaning: 603 pairs Before cleaning: 634 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 233, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 634 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 0 virtual sites Total mass 1662.888 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (44 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Before cleaning: 2499 pairs Before cleaning: 2631 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 952, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2631 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 0 virtual sites Total mass 6908.576 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (106 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Marked 124 virtual sites Added 16 dummy masses Added 26 new constraints Before cleaning: 653 pairs Before cleaning: 691 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 255, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 691 dihedrals, 51 impropers, 457 angles 650 pairs, 254 bonds and 130 virtual sites Total mass 1846.132 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (48 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Marked 132 virtual sites Added 10 dummy masses Added 19 new constraints Before cleaning: 748 pairs Before cleaning: 788 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 291, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 788 dihedrals, 72 impropers, 516 angles 736 pairs, 290 bonds and 133 virtual sites Total mass 2088.366 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (51 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Marked 123 virtual sites Added 22 dummy masses Added 35 new constraints Before cleaning: 676 pairs Before cleaning: 727 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 262, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 727 dihedrals, 56 impropers, 472 angles 667 pairs, 261 bonds and 132 virtual sites Total mass 1861.124 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (48 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Marked 111 virtual sites Added 18 dummy masses Added 31 new constraints Before cleaning: 603 pairs Before cleaning: 634 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 233, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 634 dihedrals, 48 impropers, 419 angles 597 pairs, 232 bonds and 116 virtual sites Total mass 1662.888 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Marked 447 virtual sites Added 58 dummy masses Added 101 new constraints Before cleaning: 2499 pairs Before cleaning: 2631 dihedrals Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 952, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2631 dihedrals, 208 impropers, 1704 angles 2469 pairs, 951 bonds and 462 virtual sites Total mass 6908.576 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (114 ms) [----------] 10 tests from Amber/Pdb2gmxTest (605 ms total) [----------] 1 test from AmberTip4p/Pdb2gmxTest [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/amber99sb-ildn.ff/rna.arn Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/tip4p.pdb... Read 'TIP4p ice to test that MW is handled correctly', 4 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 0 chains and 1 blocks of water and 2 residues with 4 atoms chain #res #atoms 1 ' ' 2 4 (only water) All occupancies are one Reading residue database... (Amber99sb-ildn) Processing chain 1 (4 atoms, 2 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 2 residues with 8 atoms Making bonds... Number of bonds was 4, now 4 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 2 angles 0 pairs, 4 bonds and 0 virtual sites Total mass 36.032 a.m.u. Total charge 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/tip4p.pdb. The Amber99sb-ildn force field and the tip4p water model are used. --------- ETON ESAELP ------------ [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (30 ms) [----------] 1 test from AmberTip4p/Pdb2gmxTest (30 ms total) [----------] 12 tests from Charmm/Pdb2gmxTest [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 663 dihedrals, 48 impropers, 457 angles 650 pairs, 254 bonds and 0 virtual sites Total mass 1846.115 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (48 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 778 dihedrals, 49 impropers, 516 angles 736 pairs, 290 bonds and 0 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (49 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 696 dihedrals, 39 impropers, 472 angles 667 pairs, 261 bonds and 0 virtual sites Total mass 1861.130 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 618 dihedrals, 38 impropers, 419 angles 597 pairs, 232 bonds and 0 virtual sites Total mass 1662.885 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 56 cmap torsion pairs There are 2524 dihedrals, 149 impropers, 1704 angles 2469 pairs, 951 bonds and 0 virtual sites Total mass 6908.566 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (102 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 39 pairs Before cleaning: 39 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/monomer.pdb... Read 'GLU', 9 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 9 atoms chain #res #atoms 1 'X' 1 9 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'X' (9 atoms, 1 residues) Identified residue GLU1 as a starting terminus. Identified residue GLU1 as a ending terminus. Start terminus GLU-1: NH3+ End terminus GLU-1: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 18 atoms Making bonds... Number of bonds was 17, now 17 Generating angles, dihedrals and pairs... Making cmap torsions... There are 39 dihedrals, 2 impropers, 30 angles 39 pairs, 17 bonds and 0 virtual sites Total mass 146.123 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/monomer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (34 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 124 virtual sites Added 16 dummy masses Added 26 new constraints Before cleaning: 653 pairs Before cleaning: 663 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 128 atoms chain #res #atoms 1 ' ' 16 128 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (128 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 252 atoms Making bonds... Number of bonds was 254, now 254 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 663 dihedrals, 48 impropers, 457 angles 650 pairs, 254 bonds and 130 virtual sites Total mass 1846.115 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/A.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (61 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 30 donors and 22 acceptors were found. There are 36 hydrogen bonds Will use HISE for residue 29 Will use HISE for residue 32 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS27 HIS29 SG90 NE2111 HIS29 NE2111 0.987 HIS32 NE2135 1.590 1.155 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 132 virtual sites Added 10 dummy masses Added 19 new constraints Before cleaning: 748 pairs Before cleaning: 778 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb... Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 149 atoms chain #res #atoms 1 ' ' 16 149 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (149 atoms, 16 residues) Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. Identified residue THR18 as a starting terminus. Identified residue PHE33 as a ending terminus. Start terminus THR-18: NH3+ End terminus PHE-33: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 281 atoms Making bonds... Number of bonds was 290, now 290 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 778 dihedrals, 49 impropers, 516 angles 736 pairs, 290 bonds and 133 virtual sites Total mass 2088.361 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/B.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (53 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 22 acceptors were found. There are 26 hydrogen bonds Will use HISE for residue 45 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS45 NE295 MET46 SD102 1.078 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 123 virtual sites Added 22 dummy masses Added 35 new constraints Before cleaning: 676 pairs Before cleaning: 696 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb... Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 132 atoms chain #res #atoms 1 ' ' 16 132 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (132 atoms, 16 residues) Identified residue ALA34 as a starting terminus. Identified residue ALA49 as a ending terminus. Start terminus ALA-34: NH3+ End terminus ALA-49: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 261, now 261 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 696 dihedrals, 39 impropers, 472 angles 667 pairs, 261 bonds and 132 virtual sites Total mass 1861.130 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/C.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 22 donors and 21 acceptors were found. There are 30 hydrogen bonds Will use HISE for residue 60 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS60 NE285 CYS62 SG98 0.803 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 111 virtual sites Added 18 dummy masses Added 31 new constraints Before cleaning: 603 pairs Before cleaning: 618 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb... Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 16 residues with 117 atoms chain #res #atoms 1 ' ' 16 117 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 (117 atoms, 16 residues) Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. Identified residue LYS50 as a starting terminus. Identified residue PRO65 as a ending terminus. Start terminus LYS-50: NH3+ End terminus PRO-65: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 228 atoms Making bonds... Number of bonds was 232, now 232 Generating angles, dihedrals and pairs... Making cmap torsions... There are 14 cmap torsion pairs There are 618 dihedrals, 38 impropers, 419 angles 597 pairs, 232 bonds and 116 virtual sites Total mass 1662.885 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/D.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (48 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 89 donors and 98 acceptors were found. There are 129 hydrogen bonds Will use HISE for residue 31 Will use HISE for residue 51 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS25 HIS31 HIS51 SG14 NE264 NE2226 HIS31 NE264 1.921 HIS51 NE2226 1.498 2.650 CYS80 SG477 0.207 1.984 1.570 Linking CYS-25 SG-14 and CYS-80 SG-477... Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 447 virtual sites Added 58 dummy masses Added 101 new constraints Before cleaning: 2499 pairs Before cleaning: 2524 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb... Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 58 residues with 488 atoms chain #res #atoms 1 'A' 58 488 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (488 atoms, 58 residues) Identified residue ASN24 as a starting terminus. Identified residue ARG81 as a ending terminus. Start terminus ASN-24: NH3+ End terminus ARG-81: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 936 atoms Making bonds... Number of bonds was 951, now 951 Generating angles, dihedrals and pairs... Making cmap torsions... There are 56 cmap torsion pairs There are 2524 dihedrals, 149 impropers, 1704 angles 2469 pairs, 951 bonds and 462 virtual sites Total mass 6908.566 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/E.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (114 ms) [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Marked 8 virtual sites Added 2 dummy masses Added 3 new constraints Before cleaning: 39 pairs Before cleaning: 39 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/monomer.pdb... Read 'GLU', 9 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 9 atoms chain #res #atoms 1 'X' 1 9 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'X' (9 atoms, 1 residues) Identified residue GLU1 as a starting terminus. Identified residue GLU1 as a ending terminus. Start terminus GLU-1: NH3+ End terminus GLU-1: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 18 atoms Making bonds... Number of bonds was 17, now 17 Generating angles, dihedrals and pairs... Making cmap torsions... There are 39 dihedrals, 2 impropers, 30 angles 39 pairs, 17 bonds and 9 virtual sites Total mass 146.123 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/monomer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (35 ms) [----------] 12 tests from Charmm/Pdb2gmxTest (691 ms total) [----------] 8 tests from ChainSep/Pdb2gmxTest [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 651 pairs Before cleaning: 661 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on changing chain id only (ignoring TER records). Merged chains into joint molecule definitions at 2 places. There are 1 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 16 127 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (127 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue GLU5 as a ending terminus. Identified residue PHE6 as a starting terminus. Identified residue MET12 as a ending terminus. Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus GLU-5: COO- Start terminus PHE-6: NH3+ End terminus MET-12: COO- Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 258 atoms Making bonds... Number of bonds was 258, now 258 Generating angles, dihedrals and pairs... Making cmap torsions... There are 10 cmap torsion pairs There are 661 dihedrals, 46 impropers, 463 angles 648 pairs, 258 bonds and 0 virtual sites Total mass 1882.146 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (47 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 123 pairs Before cleaning: 123 dihedrals Analysing hydrogen-bonding network for automated assignment of histidine protonation. 10 donors and 7 acceptors were found. There are 7 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS8 NE223 MET12 SD55 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 317 pairs Before cleaning: 322 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 211 pairs Before cleaning: 216 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on changing chain id only (ignoring TER records). There are 3 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 4 28 2 'B' 7 58 3 'C' 5 41 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (28 atoms, 4 residues) Identified residue ALA2 as a starting terminus. Identified residue GLU5 as a ending terminus. Start terminus ALA-2: NH3+ End terminus GLU-5: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 4 residues with 51 atoms Chain time... Making bonds... Number of bonds was 50, now 50 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2 cmap torsion pairs There are 123 dihedrals, 9 impropers, 88 angles 123 pairs, 50 bonds and 0 virtual sites Total mass 434.421 a.m.u. Total charge -2.000 e Writing topology Processing chain 2 'B' (58 atoms, 7 residues) Identified residue PHE6 as a starting terminus. Identified residue MET12 as a ending terminus. Start terminus PHE-6: NH3+ End terminus MET-12: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 7 residues with 124 atoms Chain time... Making bonds... Number of bonds was 125, now 125 Generating angles, dihedrals and pairs... Making cmap torsions... There are 5 cmap torsion pairs There are 322 dihedrals, 19 impropers, 227 angles 314 pairs, 125 bonds and 0 virtual sites Total mass 846.083 a.m.u. Total charge 1.000 e Writing topology Processing chain 3 'C' (41 atoms, 5 residues) Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 83 atoms Chain time... Making bonds... Number of bonds was 83, now 83 Generating angles, dihedrals and pairs... Making cmap torsions... There are 3 cmap torsion pairs There are 216 dihedrals, 18 impropers, 148 angles 211 pairs, 83 bonds and 0 virtual sites Total mass 601.643 a.m.u. Total charge 1.000 e Writing topology Including chain 1 in system: 51 atoms 4 residues Including chain 2 in system: 124 atoms 7 residues Including chain 3 in system: 83 atoms 5 residues Now there are 258 atoms and 16 residues Total mass in system 1882.146 a.m.u. Total charge in system 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (54 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 651 pairs Before cleaning: 661 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records only (ignoring chain id). Merged chains into joint molecule definitions at 2 places. There are 1 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 16 127 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (127 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue ILE9 as a ending terminus. Identified residue LYS10 as a starting terminus. Identified residue MET12 as a ending terminus. Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ILE-9: COO- Start terminus LYS-10: NH3+ End terminus MET-12: COO- Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 258 atoms Making bonds... Number of bonds was 258, now 258 Generating angles, dihedrals and pairs... Making cmap torsions... There are 10 cmap torsion pairs There are 661 dihedrals, 46 impropers, 463 angles 648 pairs, 258 bonds and 0 virtual sites Total mass 1882.146 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (47 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 10 donors and 12 acceptors were found. There are 13 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 SG9 HIS8 NE251 1.055 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 288 pairs Before cleaning: 293 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 152 pairs Before cleaning: 152 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 211 pairs Before cleaning: 216 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records only (ignoring chain id). There are 3 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 8 61 2 'B' 3 25 3 'C' 5 41 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (61 atoms, 8 residues) Identified residue ALA2 as a starting terminus. Identified residue ILE9 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ILE-9: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 8 residues with 114 atoms Chain time... Making bonds... Number of bonds was 115, now 115 Generating angles, dihedrals and pairs... Making cmap torsions... There are 6 cmap torsion pairs There are 293 dihedrals, 23 impropers, 203 angles 285 pairs, 115 bonds and 0 virtual sites Total mass 888.952 a.m.u. Total charge -2.000 e Writing topology Processing chain 2 'B' (25 atoms, 3 residues) Identified residue LYS10 as a starting terminus. Identified residue MET12 as a ending terminus. Start terminus LYS-10: NH3+ End terminus MET-12: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 61 atoms Chain time... Making bonds... Number of bonds was 60, now 60 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 152 dihedrals, 5 impropers, 112 angles 152 pairs, 60 bonds and 0 virtual sites Total mass 391.552 a.m.u. Total charge 1.000 e Writing topology Processing chain 3 'C' (41 atoms, 5 residues) Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 83 atoms Chain time... Making bonds... Number of bonds was 83, now 83 Generating angles, dihedrals and pairs... Making cmap torsions... There are 3 cmap torsion pairs There are 216 dihedrals, 18 impropers, 148 angles 211 pairs, 83 bonds and 0 virtual sites Total mass 601.643 a.m.u. Total charge 1.000 e Writing topology Including chain 1 in system: 114 atoms 8 residues Including chain 2 in system: 61 atoms 3 residues Including chain 3 in system: 83 atoms 5 residues Now there are 258 atoms and 16 residues Total mass in system 1882.146 a.m.u. Total charge in system 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (52 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 650 pairs Before cleaning: 660 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merged chains into joint molecule definitions at 3 places. There are 1 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 16 127 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (127 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue GLU5 as a ending terminus. Identified residue PHE6 as a starting terminus. Identified residue ILE9 as a ending terminus. Identified residue LYS10 as a starting terminus. Identified residue MET12 as a ending terminus. Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus GLU-5: COO- Start terminus PHE-6: NH3+ End terminus ILE-9: COO- Start terminus LYS-10: NH3+ End terminus MET-12: COO- Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 261 atoms Making bonds... Number of bonds was 260, now 260 Generating angles, dihedrals and pairs... Making cmap torsions... There are 8 cmap torsion pairs There are 660 dihedrals, 45 impropers, 466 angles 647 pairs, 260 bonds and 0 virtual sites Total mass 1900.162 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (48 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 123 pairs Before cleaning: 123 dihedrals Analysing hydrogen-bonding network for automated assignment of histidine protonation. 6 donors and 4 acceptors were found. There are 3 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 164 pairs Before cleaning: 169 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 152 pairs Before cleaning: 152 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 211 pairs Before cleaning: 216 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 4 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 4 28 2 'B' 4 33 3 'B' 3 25 4 'C' 5 41 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (28 atoms, 4 residues) Identified residue ALA2 as a starting terminus. Identified residue GLU5 as a ending terminus. Start terminus ALA-2: NH3+ End terminus GLU-5: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 4 residues with 51 atoms Chain time... Making bonds... Number of bonds was 50, now 50 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2 cmap torsion pairs There are 123 dihedrals, 9 impropers, 88 angles 123 pairs, 50 bonds and 0 virtual sites Total mass 434.421 a.m.u. Total charge -2.000 e Writing topology Processing chain 2 'B' (33 atoms, 4 residues) Identified residue PHE6 as a starting terminus. Identified residue ILE9 as a ending terminus. Start terminus PHE-6: NH3+ End terminus ILE-9: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 4 residues with 66 atoms Chain time... Making bonds... Number of bonds was 67, now 67 Generating angles, dihedrals and pairs... Making cmap torsions... There are 2 cmap torsion pairs There are 169 dihedrals, 13 impropers, 118 angles 161 pairs, 67 bonds and 0 virtual sites Total mass 472.547 a.m.u. Total charge 0.000 e Writing topology Processing chain 3 'B' (25 atoms, 3 residues) Identified residue LYS10 as a starting terminus. Identified residue MET12 as a ending terminus. Start terminus LYS-10: NH3+ End terminus MET-12: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 61 atoms Chain time... Making bonds... Number of bonds was 60, now 60 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 152 dihedrals, 5 impropers, 112 angles 152 pairs, 60 bonds and 0 virtual sites Total mass 391.552 a.m.u. Total charge 1.000 e Writing topology Processing chain 4 'C' (41 atoms, 5 residues) Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 83 atoms Chain time... Making bonds... Number of bonds was 83, now 83 Generating angles, dihedrals and pairs... Making cmap torsions... There are 3 cmap torsion pairs There are 216 dihedrals, 18 impropers, 148 angles 211 pairs, 83 bonds and 0 virtual sites Total mass 601.643 a.m.u. Total charge 1.000 e Writing topology Including chain 1 in system: 51 atoms 4 residues Including chain 2 in system: 66 atoms 4 residues Including chain 3 in system: 61 atoms 3 residues Including chain 4 in system: 83 atoms 5 residues Now there are 261 atoms and 16 residues Total mass in system 1900.162 a.m.u. Total charge in system 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (57 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 25 donors and 23 acceptors were found. There are 41 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 652 pairs Before cleaning: 662 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records and chain id changing. Merged chains into joint molecule definitions at 1 places. There are 1 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 16 127 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (127 atoms, 16 residues) Identified residue ALA2 as a starting terminus. Identified residue MET12 as a ending terminus. Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ALA-2: NH3+ End terminus MET-12: COO- Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 255 atoms Making bonds... Number of bonds was 256, now 256 Generating angles, dihedrals and pairs... Making cmap torsions... There are 12 cmap torsion pairs There are 662 dihedrals, 47 impropers, 460 angles 649 pairs, 256 bonds and 0 virtual sites Total mass 1864.131 a.m.u. Total charge 0.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (46 ms) [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb Analysing hydrogen-bonding network for automated assignment of histidine protonation. 14 donors and 15 acceptors were found. There are 20 hydrogen bonds Will use HISE for residue 8 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS8 SG9 NE251 HIS8 NE251 1.055 MET12 SD83 0.763 0.990 Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 441 pairs Before cleaning: 446 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 211 pairs Before cleaning: 216 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb... Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms Analyzing pdb file Splitting chemical chains based on TER records and chain id changing. There are 2 chains and 0 blocks of water and 16 residues with 127 atoms chain #res #atoms 1 'A' 11 86 2 'C' 5 41 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (86 atoms, 11 residues) Identified residue ALA2 as a starting terminus. Identified residue MET12 as a ending terminus. Start terminus ALA-2: NH3+ End terminus MET-12: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 11 residues with 172 atoms Chain time... Making bonds... Number of bonds was 173, now 173 Generating angles, dihedrals and pairs... Making cmap torsions... There are 9 cmap torsion pairs There are 446 dihedrals, 29 impropers, 312 angles 438 pairs, 173 bonds and 0 virtual sites Total mass 1262.488 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'C' (41 atoms, 5 residues) Identified residue ASN13 as a starting terminus. Identified residue SER17 as a ending terminus. Start terminus ASN-13: NH3+ End terminus SER-17: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 83 atoms Chain time... Making bonds... Number of bonds was 83, now 83 Generating angles, dihedrals and pairs... Making cmap torsions... There are 3 cmap torsion pairs There are 216 dihedrals, 18 impropers, 148 angles 211 pairs, 83 bonds and 0 virtual sites Total mass 601.643 a.m.u. Total charge 1.000 e Writing topology Including chain 1 in system: 172 atoms 11 residues Including chain 2 in system: 83 atoms 5 residues Now there are 255 atoms and 16 residues Total mass in system 1864.131 a.m.u. Total charge in system 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/chainTer.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (48 ms) [----------] 8 tests from ChainSep/Pdb2gmxTest (403 ms total) [----------] 4 tests from ChainChanges/Pdb2gmxTest [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 83 pairs Before cleaning: 83 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 145 pairs Before cleaning: 150 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb... Read 'Fragments of peptides and ions', 47 atoms Analyzing pdb file Splitting chemical chains based on changing chain id only (ignoring TER records). There are 2 chains and 0 blocks of water and 6 residues with 47 atoms chain #res #atoms 1 'A' 3 19 2 'B' 3 28 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (19 atoms, 3 residues) Identified residue ALA2 as a starting terminus. Identified residue ASP4 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ASP-4: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 36 atoms Chain time... Making bonds... Number of bonds was 35, now 35 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 83 dihedrals, 6 impropers, 61 angles 83 pairs, 35 bonds and 0 virtual sites Total mass 306.314 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'B' (28 atoms, 3 residues) Identified residue THR18 as a starting terminus. Identified residue TRP20 as a ending terminus. Start terminus THR-18: NH3+ End terminus TRP-20: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 57 atoms Chain time... Making bonds... Number of bonds was 58, now 58 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 150 dihedrals, 5 impropers, 103 angles 142 pairs, 58 bonds and 0 virtual sites Total mass 404.468 a.m.u. Total charge -0.000 e Writing topology Including chain 1 in system: 36 atoms 3 residues Including chain 2 in system: 57 atoms 3 residues Now there are 93 atoms and 6 residues Total mass in system 710.782 a.m.u. Total charge in system -1.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (45 ms) [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 83 pairs Before cleaning: 83 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 145 pairs Before cleaning: 150 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb... Read 'Fragments of peptides and ions', 47 atoms Analyzing pdb file Splitting chemical chains based on TER records only (ignoring chain id). There are 2 chains and 0 blocks of water and 6 residues with 47 atoms chain #res #atoms 1 'A' 3 19 2 'B' 3 28 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (19 atoms, 3 residues) Identified residue ALA2 as a starting terminus. Identified residue ASP4 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ASP-4: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 36 atoms Chain time... Making bonds... Number of bonds was 35, now 35 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 83 dihedrals, 6 impropers, 61 angles 83 pairs, 35 bonds and 0 virtual sites Total mass 306.314 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'B' (28 atoms, 3 residues) Identified residue THR18 as a starting terminus. Identified residue TRP20 as a ending terminus. Start terminus THR-18: NH3+ End terminus TRP-20: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 57 atoms Chain time... Making bonds... Number of bonds was 58, now 58 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 150 dihedrals, 5 impropers, 103 angles 142 pairs, 58 bonds and 0 virtual sites Total mass 404.468 a.m.u. Total charge -0.000 e Writing topology Including chain 1 in system: 36 atoms 3 residues Including chain 2 in system: 57 atoms 3 residues Now there are 93 atoms and 6 residues Total mass in system 710.782 a.m.u. Total charge in system -1.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (42 ms) [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 83 pairs Before cleaning: 83 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 145 pairs Before cleaning: 150 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb... Read 'Fragments of peptides and ions', 47 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 6 residues with 47 atoms chain #res #atoms 1 'A' 3 19 2 'B' 3 28 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (19 atoms, 3 residues) Identified residue ALA2 as a starting terminus. Identified residue ASP4 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ASP-4: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 36 atoms Chain time... Making bonds... Number of bonds was 35, now 35 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 83 dihedrals, 6 impropers, 61 angles 83 pairs, 35 bonds and 0 virtual sites Total mass 306.314 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'B' (28 atoms, 3 residues) Identified residue THR18 as a starting terminus. Identified residue TRP20 as a ending terminus. Start terminus THR-18: NH3+ End terminus TRP-20: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 57 atoms Chain time... Making bonds... Number of bonds was 58, now 58 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 150 dihedrals, 5 impropers, 103 angles 142 pairs, 58 bonds and 0 virtual sites Total mass 404.468 a.m.u. Total charge -0.000 e Writing topology Including chain 1 in system: 36 atoms 3 residues Including chain 2 in system: 57 atoms 3 residues Now there are 93 atoms and 6 residues Total mass in system 710.782 a.m.u. Total charge in system -1.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (47 ms) [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 83 pairs Before cleaning: 83 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 145 pairs Before cleaning: 150 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb... Read 'Fragments of peptides and ions', 47 atoms Analyzing pdb file Splitting chemical chains based on TER records and chain id changing. There are 2 chains and 0 blocks of water and 6 residues with 47 atoms chain #res #atoms 1 'A' 3 19 2 'B' 3 28 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (19 atoms, 3 residues) Identified residue ALA2 as a starting terminus. Identified residue ASP4 as a ending terminus. Start terminus ALA-2: NH3+ End terminus ASP-4: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 36 atoms Chain time... Making bonds... Number of bonds was 35, now 35 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 83 dihedrals, 6 impropers, 61 angles 83 pairs, 35 bonds and 0 virtual sites Total mass 306.314 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'B' (28 atoms, 3 residues) Identified residue THR18 as a starting terminus. Identified residue TRP20 as a ending terminus. Start terminus THR-18: NH3+ End terminus TRP-20: COO- Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 3 residues with 57 atoms Chain time... Making bonds... Number of bonds was 58, now 58 Generating angles, dihedrals and pairs... Making cmap torsions... There are 1 cmap torsion pairs There are 150 dihedrals, 5 impropers, 103 angles 142 pairs, 58 bonds and 0 virtual sites Total mass 404.468 a.m.u. Total charge -0.000 e Writing topology Including chain 1 in system: 36 atoms 3 residues Including chain 2 in system: 57 atoms 3 residues Now there are 93 atoms and 6 residues Total mass in system 710.782 a.m.u. Total charge in system -1.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/fragments.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (44 ms) [----------] 4 tests from ChainChanges/Pdb2gmxTest (179 ms total) [----------] 4 tests from Cyclic/Pdb2gmxTest [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b WARNING: all CONECT records are ignored Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 6040 pairs Before cleaning: 6605 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 6040 pairs Before cleaning: 6605 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. Moved all the water blocks to the end There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms chain #res #atoms 1 'P' 71 1527 2 'Q' 71 1527 3 'Q' 7 7 4 ' ' 10 10 (only water) 5 ' ' 16 16 (only water) All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'P' (1527 atoms, 71 residues) Identified residue G1 as a starting terminus. Identified residue U71 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 71 residues with 2297 atoms Chain time... Making bonds... Number of bonds was 2481, now 2481 Generating angles, dihedrals and pairs... Making cmap torsions... There are 6605 dihedrals, 183 impropers, 4434 angles 5827 pairs, 2481 bonds and 0 virtual sites Total mass 22984.514 a.m.u. Total charge -71.000 e Writing topology Processing chain 2 'Q' (1527 atoms, 71 residues) Identified residue G1 as a starting terminus. Identified residue U71 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 71 residues with 2297 atoms Chain time... Making bonds... Number of bonds was 2481, now 2481 Generating angles, dihedrals and pairs... Making cmap torsions... There are 6605 dihedrals, 183 impropers, 4434 angles 5827 pairs, 2481 bonds and 0 virtual sites Total mass 22984.514 a.m.u. Total charge -71.000 e Writing topology Processing chain 3 'Q' (7 atoms, 7 residues) Residue MG72 has type 'Ion', assuming it is not linked into a chain. Residue MG73 has type 'Ion', assuming it is not linked into a chain. Residue MG74 has type 'Ion', assuming it is not linked into a chain. Residue MG75 has type 'Ion', assuming it is not linked into a chain. Residue MG76 has type 'Ion', assuming it is not linked into a chain. Disabling further notes about ions. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 7 residues with 7 atoms Chain time... Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 0 angles 0 pairs, 0 bonds and 0 virtual sites Total mass 170.135 a.m.u. Total charge 14.000 e Writing topology Processing chain 4 (10 atoms, 10 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 10 residues with 30 atoms Making bonds... Number of bonds was 30, now 30 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 30 angles 0 pairs, 30 bonds and 0 virtual sites Total mass 180.154 a.m.u. Total charge 0.000 e Processing chain 5 (16 atoms, 16 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 48 atoms Making bonds... Number of bonds was 48, now 48 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 48 angles 0 pairs, 48 bonds and 0 virtual sites Total mass 288.246 a.m.u. Total charge 0.000 e Including chain 1 in system: 2297 atoms 71 residues Including chain 2 in system: 2297 atoms 71 residues Including chain 3 in system: 7 atoms 7 residues Including chain 4 in system: 30 atoms 10 residues Including chain 5 in system: 48 atoms 16 residues Now there are 4679 atoms and 175 residues Total mass in system 46607.562 a.m.u. Total charge in system -128.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (581 ms) [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 2325 pairs Before cleaning: 2325 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... Read 'CARNOCYCLIN-A', 413 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 60 residues with 413 atoms chain #res #atoms 1 'A' 60 413 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (413 atoms, 60 residues) Identified residue LEU1 as a starting terminus. Identified residue LEU60 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 60 residues with 878 atoms Making bonds... Number of bonds was 880, now 880 Generating angles, dihedrals and pairs... Making cmap torsions... There are 59 cmap torsion pairs There are 2325 dihedrals, 137 impropers, 1614 angles 2319 pairs, 880 bonds and 0 virtual sites Total mass 5866.087 a.m.u. Total charge 4.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (100 ms) [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b WARNING: all CONECT records are ignored All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 12080 pairs Before cleaning: 13210 dihedrals 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Moved all the water blocks to the end Merged chains into joint molecule definitions at 2 places. There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms chain #res #atoms 1 'P' 149 3061 2 ' ' 10 10 (only water) 3 ' ' 16 16 (only water) All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'P' (3061 atoms, 149 residues) Identified residue G1 as a starting terminus. Identified residue U71 as a ending terminus. Identified residue G1 as a starting terminus. Identified residue U71 as a ending terminus. Residue MG72 has type 'Ion', assuming it is not linked into a chain. Residue MG73 has type 'Ion', assuming it is not linked into a chain. Residue MG74 has type 'Ion', assuming it is not linked into a chain. Residue MG75 has type 'Ion', assuming it is not linked into a chain. Residue MG76 has type 'Ion', assuming it is not linked into a chain. Disabling further notes about ions. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 149 residues with 4601 atoms Making bonds... Number of bonds was 4962, now 4962 Generating angles, dihedrals and pairs... Making cmap torsions... There are 13210 dihedrals, 366 impropers, 8868 angles 11654 pairs, 4962 bonds and 0 virtual sites Total mass 46139.162 a.m.u. Total charge -128.000 e Writing topology Processing chain 2 (10 atoms, 10 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 10 residues with 30 atoms Making bonds... Number of bonds was 30, now 30 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 30 angles 0 pairs, 30 bonds and 0 virtual sites Total mass 180.154 a.m.u. Total charge 0.000 e Processing chain 3 (16 atoms, 16 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 16 residues with 48 atoms Making bonds... Number of bonds was 48, now 48 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 48 angles 0 pairs, 48 bonds and 0 virtual sites Total mass 288.246 a.m.u. Total charge 0.000 e Including chain 1 in system: 4601 atoms 149 residues Including chain 2 in system: 30 atoms 10 residues Including chain 3 in system: 48 atoms 16 residues Now there are 4679 atoms and 175 residues Total mass in system 46607.562 a.m.u. Total charge in system -128.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (1147 ms) [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.r2b Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.r2b All occupancies are one Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/atomtypes.atp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.rtp Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/lipids.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.hdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.n.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.c.tdb Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.c.tdb 8 out of 8 lines of specbond.dat converted successfully Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/aminoacids.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/dna.arn Opening force field file ${WORKDIR}/gromacs-2022/share/top/charmm27.ff/rna.arn Before cleaning: 2325 pairs Before cleaning: 2325 dihedrals Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Reading ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... Read 'CARNOCYCLIN-A', 413 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 60 residues with 413 atoms chain #res #atoms 1 'A' 60 413 All occupancies are one Reading residue database... (Charmm27) Processing chain 1 'A' (413 atoms, 60 residues) Identified residue LEU1 as a starting terminus. Identified residue LEU60 as a ending terminus. Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 60 residues with 878 atoms Making bonds... Number of bonds was 880, now 880 Generating angles, dihedrals and pairs... Making cmap torsions... There are 59 cmap torsion pairs There are 2325 dihedrals, 137 impropers, 1614 angles 2319 pairs, 880 bonds and 0 virtual sites Total mass 5866.087 a.m.u. Total charge 4.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: ${WORKDIR}/gromacs-2022/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. The Charmm27 force field and the tip3p water model are used. --------- ETON ESAELP ------------ [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (104 ms) [----------] 4 tests from Cyclic/Pdb2gmxTest (1933 ms total) [----------] Global test environment tear-down [==========] 39 tests from 6 test suites ran. (3845 ms total) [ PASSED ] 39 tests. Test time = 4.53 sec ---------------------------------------------------------- Test Passed. "Pdb2gmx3Test" end time: Feb 22 23:21 EST "Pdb2gmx3Test" time elapsed: 00:00:04 ---------------------------------------------------------- 54/90 Testing: CorrelationsTest 54/90 Test: CorrelationsTest Command: "${WORKDIR}/gromacs-2022/build/bin/correlations-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/CorrelationsTest.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/correlationfunctions/tests "CorrelationsTest" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 21 tests from 3 test suites. [----------] Global test environment set-up. [----------] 10 tests from AutocorrTest [ RUN ] AutocorrTest.EacNormal [ OK ] AutocorrTest.EacNormal (1749 ms) [ RUN ] AutocorrTest.EacNoNormalize [ OK ] AutocorrTest.EacNoNormalize (1075 ms) [ RUN ] AutocorrTest.EacCos [ OK ] AutocorrTest.EacCos (2748 ms) [ RUN ] AutocorrTest.EacVector [ OK ] AutocorrTest.EacVector (3528 ms) [ RUN ] AutocorrTest.EacRcross [ OK ] AutocorrTest.EacRcross (528 ms) [ RUN ] AutocorrTest.EacP0 [ OK ] AutocorrTest.EacP0 (3305 ms) [ RUN ] AutocorrTest.EacP1 [ OK ] AutocorrTest.EacP1 (3100 ms) [ RUN ] AutocorrTest.EacP2 [ OK ] AutocorrTest.EacP2 (7470 ms) [ RUN ] AutocorrTest.EacP3 [ OK ] AutocorrTest.EacP3 (195 ms) [ RUN ] AutocorrTest.EacP4 [ OK ] AutocorrTest.EacP4 (2898 ms) [----------] 10 tests from AutocorrTest (26603 ms total) [----------] 10 tests from ExpfitTest [ RUN ] ExpfitTest.EffnEXP1 [ OK ] ExpfitTest.EffnEXP1 (1 ms) [ RUN ] ExpfitTest.EffnEXP2 [ OK ] ExpfitTest.EffnEXP2 (0 ms) [ RUN ] ExpfitTest.EffnEXPEXP [ OK ] ExpfitTest.EffnEXPEXP (1 ms) [ RUN ] ExpfitTest.EffnEXP5 [ OK ] ExpfitTest.EffnEXP5 (3 ms) [ RUN ] ExpfitTest.EffnEXP7 [ OK ] ExpfitTest.EffnEXP7 (2 ms) [ RUN ] ExpfitTest.EffnEXP9 [ OK ] ExpfitTest.EffnEXP9 (11 ms) [ RUN ] ExpfitTest.EffnERF [ OK ] ExpfitTest.EffnERF (1 ms) [ RUN ] ExpfitTest.EffnERREST [ OK ] ExpfitTest.EffnERREST (1 ms) [ RUN ] ExpfitTest.EffnVAC [ OK ] ExpfitTest.EffnVAC (4 ms) [ RUN ] ExpfitTest.EffnPRES [ OK ] ExpfitTest.EffnPRES (11 ms) [----------] 10 tests from ExpfitTest (39 ms total) [----------] 1 test from ManyAutocorrelationTest [ RUN ] ManyAutocorrelationTest.Empty [ OK ] ManyAutocorrelationTest.Empty (0 ms) [----------] 1 test from ManyAutocorrelationTest (0 ms total) [----------] Global test environment tear-down [==========] 21 tests from 3 test suites ran. (27402 ms total) [ PASSED ] 21 tests. Test time = 28.09 sec ---------------------------------------------------------- Test Passed. "CorrelationsTest" end time: Feb 22 23:21 EST "CorrelationsTest" time elapsed: 00:00:28 ---------------------------------------------------------- 55/90 Testing: AnalysisDataUnitTests 55/90 Test: AnalysisDataUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/analysisdata-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/AnalysisDataUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/analysisdata/tests "AnalysisDataUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 69 tests from 14 test suites. [----------] Global test environment set-up. [----------] 3 tests from AnalysisDataInitializationTest [ RUN ] AnalysisDataInitializationTest.BasicInitialization [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) [----------] 8 tests from AnalysisDataCommonTest/1 (2 ms total) [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) [----------] 8 tests from AnalysisDataCommonTest/3 (2 ms total) [----------] 4 tests from AnalysisArrayDataTest [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) [ RUN ] AnalysisArrayDataTest.StorageWorks [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) [ RUN ] AnalysisArrayDataTest.CanSetXAxis [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) [----------] 4 tests from AnalysisArrayDataTest (0 ms total) [----------] 6 tests from AverageModuleTest [ RUN ] AverageModuleTest.BasicTest [ OK ] AverageModuleTest.BasicTest (0 ms) [ RUN ] AverageModuleTest.HandlesMultipointData [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) [ RUN ] AverageModuleTest.HandlesMultipleDataSets [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) [ RUN ] AverageModuleTest.HandlesDataSetAveraging [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) [ RUN ] AverageModuleTest.CanCustomizeXAxis [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) [----------] 6 tests from AverageModuleTest (5 ms total) [----------] 2 tests from FrameAverageModuleTest [ RUN ] FrameAverageModuleTest.BasicTest [ OK ] FrameAverageModuleTest.BasicTest (0 ms) [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) [----------] 2 tests from FrameAverageModuleTest (1 ms total) [----------] 7 tests from AnalysisHistogramSettingsTest [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) [----------] 2 tests from SimpleHistogramModuleTest [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) [----------] 2 tests from SimpleHistogramModuleTest (2 ms total) [----------] 3 tests from WeightedHistogramModuleTest [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) [----------] 3 tests from WeightedHistogramModuleTest (3 ms total) [----------] 3 tests from BinAverageModuleTest [ RUN ] BinAverageModuleTest.ComputesCorrectly [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) [----------] 3 tests from BinAverageModuleTest (2 ms total) [----------] 4 tests from AbstractAverageHistogramTest [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) [----------] 4 tests from AbstractAverageHistogramTest (3 ms total) [----------] 3 tests from LifetimeModuleTest [ RUN ] LifetimeModuleTest.BasicTest [ OK ] LifetimeModuleTest.BasicTest (0 ms) [ RUN ] LifetimeModuleTest.CumulativeTest [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) [----------] 3 tests from LifetimeModuleTest (2 ms total) [----------] Global test environment tear-down [==========] 69 tests from 14 test suites ran. (33 ms total) [ PASSED ] 69 tests. Test time = 0.72 sec ---------------------------------------------------------- Test Passed. "AnalysisDataUnitTests" end time: Feb 22 23:21 EST "AnalysisDataUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 56/90 Testing: CoordinateIOTests 56/90 Test: CoordinateIOTests Command: "${WORKDIR}/gromacs-2022/build/bin/coordinateio-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/CoordinateIOTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/coordinateio/tests "CoordinateIOTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 64 tests from 19 test suites. [----------] Global test environment set-up. [----------] 1 test from OutputSelectorDeathTest [ RUN ] OutputSelectorDeathTest.RejectsBadSelection WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] OutputSelectorDeathTest.RejectsBadSelection (6 ms) [----------] 1 test from OutputSelectorDeathTest (6 ms total) [----------] 5 tests from TrajectoryFrameWriterTest [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (3 ms) [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (3 ms) [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (3 ms) [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (6 ms) [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) [----------] 5 tests from TrajectoryFrameWriterTest (17 ms total) [----------] 5 tests from OutputAdapterContainer [ RUN ] OutputAdapterContainer.MakeEmpty [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) [ RUN ] OutputAdapterContainer.AddAdapter [ OK ] OutputAdapterContainer.AddAdapter (0 ms) [ RUN ] OutputAdapterContainer.RejectBadAdapter [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) [----------] 5 tests from OutputAdapterContainer (0 ms total) [----------] 5 tests from FlagTest [ RUN ] FlagTest.CanSetSimpleFlag [ OK ] FlagTest.CanSetSimpleFlag (0 ms) [ RUN ] FlagTest.CanAddNewBox [ OK ] FlagTest.CanAddNewBox (0 ms) [ RUN ] FlagTest.SetsImplicitPrecisionChange [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) [ RUN ] FlagTest.SetsImplicitStartTimeChange [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) [ RUN ] FlagTest.SetsImplicitTimeStepChange [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) [----------] 5 tests from FlagTest (0 ms total) [----------] 5 tests from SetAtomsTest [ RUN ] SetAtomsTest.RemovesExistingAtoms WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SetAtomsTest.RemovesExistingAtoms (3 ms) [ RUN ] SetAtomsTest.AddsNewAtoms WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SetAtomsTest.AddsNewAtoms (3 ms) [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (3 ms) [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (3 ms) [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (3 ms) [----------] 5 tests from SetAtomsTest (17 ms total) [----------] 2 tests from SetBothTimeTest [ RUN ] SetBothTimeTest.StartTimeZeroWorks [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) [----------] 2 tests from SetBothTimeTest (0 ms total) [----------] 2 tests from SetStartTimeTest [ RUN ] SetStartTimeTest.WorksWithNonZeroStart [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) [ RUN ] SetStartTimeTest.WorksWithZeroStart [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) [----------] 2 tests from SetStartTimeTest (0 ms total) [----------] 1 test from SetTimeStepTest [ RUN ] SetTimeStepTest.SetTimeStepWorks [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) [----------] 1 test from SetTimeStepTest (0 ms total) [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (3 ms) [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (3 ms) [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (3 ms) [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (3 ms) [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (3 ms) [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (3 ms) [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (20 ms total) [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (3 ms) [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (3 ms) [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (3 ms) [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (10 ms total) [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (7 ms) [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (7 ms) [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (7 ms) [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (7 ms) [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (29 ms total) [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (3 ms) [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (3 ms) [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (3 ms) [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (10 ms total) [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) [----------] 2 tests from ModuleSupported/SetForceSupportedFiles [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (3 ms) [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (3 ms) [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (6 ms total) [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (3 ms) [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (3 ms) [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (6 ms total) [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) [----------] 4 tests from ModuleSupported/NoOptionalOutput [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (3 ms) [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (3 ms) [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (3 ms) [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (3 ms) [----------] 4 tests from ModuleSupported/NoOptionalOutput (13 ms total) [----------] Global test environment tear-down [==========] 64 tests from 19 test suites ran. (140 ms total) [ PASSED ] 64 tests. Test time = 0.82 sec ---------------------------------------------------------- Test Passed. "CoordinateIOTests" end time: Feb 22 23:21 EST "CoordinateIOTests" time elapsed: 00:00:00 ---------------------------------------------------------- 57/90 Testing: TrajectoryAnalysisUnitTests 57/90 Test: TrajectoryAnalysisUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/trajectoryanalysis-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests "TrajectoryAnalysisUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 96 tests from 17 test suites. [----------] Global test environment set-up. [----------] 11 tests from AngleModuleTest [ RUN ] AngleModuleTest.ComputesSimpleAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesSimpleAngles (5 ms) [ RUN ] AngleModuleTest.ComputesDihedrals Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) [ RUN ] AngleModuleTest.ComputesVectorPairAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (3 ms) [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (3 ms) [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles Reading frames from gro file 'Test system for different angles', 33 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (4 ms) [ RUN ] AngleModuleTest.ComputesMultipleAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) [ RUN ] AngleModuleTest.HandlesDynamicSelections Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (3 ms) [----------] 11 tests from AngleModuleTest (43 ms total) [----------] 5 tests from ClustsizeTest [ RUN ] ClustsizeTest.NoMolDefaultCutoff Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements There is one group in the index '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Total number of atoms in clusters = 24 cmid: 2, cmax: 4, max_size: 6 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (11 ms) [ RUN ] ClustsizeTest.NoMolShortCutoff Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements There is one group in the index '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Total number of atoms in clusters = 24 cmid: 1, cmax: 6, max_size: 6 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (9 ms) [ RUN ] ClustsizeTest.MolDefaultCutoff Reading frames from pdb file Reading frame 0 time 0.000 Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Total number of atoms in clusters = 8 cmid: 2, cmax: 4, max_size: 2 50%100%cmid: 2, cmax: 6, max_size: 2 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (10 ms) [ RUN ] ClustsizeTest.MolShortCutoff Reading frames from pdb file Reading frame 0 time 0.000 Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Total number of atoms in clusters = 8 cmid: 1, cmax: 6, max_size: 2 50%100%cmid: 2, cmax: 6, max_size: 2 50%100%[ OK ] ClustsizeTest.MolShortCutoff (9 ms) [ RUN ] ClustsizeTest.MolCSize Reading frames from pdb file Reading frame 0 time 0.000 Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Total number of atoms in clusters = 8 cmid: 2, cmax: 4, max_size: 2 50%100%cmid: 2, cmax: 6, max_size: 2 50%100%[ OK ] ClustsizeTest.MolCSize (11 ms) [----------] 5 tests from ClustsizeTest (52 ms total) [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory Reading frames from gro file 'Test system', 8 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (4 ms) [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset Reading frames from gro file 'Test system', 8 atoms. Reading frame 0 time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (5 ms) [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (11 ms total) [----------] 4 tests from ConvertTrjModuleTest [ RUN ] ConvertTrjModuleTest.WritesNormalOutput Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading frame 0 time 0.000 Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 [ OK ] ConvertTrjModuleTest.WritesNormalOutput (7 ms) [ RUN ] ConvertTrjModuleTest.WritesAtomSubset Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading frame 0 time 0.000 Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 [ OK ] ConvertTrjModuleTest.WritesAtomSubset (8 ms) [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (4 ms) [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (4 ms) [----------] 4 tests from ConvertTrjModuleTest (24 ms total) [----------] 6 tests from DistanceModuleTest [ RUN ] DistanceModuleTest.ComputesDistances Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. atomname S1 S2: Number of samples: 5 Average distance: 1.43246 nm Standard deviation: 0.96700 nm [ OK ] DistanceModuleTest.ComputesDistances (4 ms) [ RUN ] DistanceModuleTest.ComputesMultipleDistances Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. atomname S1 S2: Number of samples: 5 Average distance: 1.43246 nm Standard deviation: 0.96700 nm resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: Number of samples: 4 Average distance: 1.81066 nm Standard deviation: 0.79289 nm [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) [ RUN ] DistanceModuleTest.HandlesDynamicSelections Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. atomname S1 S2 and res_cog x < 2.8: Number of samples: 3 Average distance: 1.72076 nm Standard deviation: 1.24839 nm [ OK ] DistanceModuleTest.HandlesDynamicSelections (4 ms) [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. Contacts: Number of samples: 2 Average distance: 1.00000 nm Standard deviation: 0.00000 nm [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (8 ms) [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. SuccessiveContacts: Number of samples: 2 Average distance: 1.00000 nm Standard deviation: 0.00000 nm [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (7 ms) [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. ManyContacts: Number of samples: 10 Average distance: 1.82913 nm Standard deviation: 0.78478 nm [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (7 ms) [----------] 6 tests from DistanceModuleTest (37 ms total) [----------] 2 tests from ExtractClusterModuleTest [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms trr version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 Analyzed 26 frames, last time 0.050 There are 8 clusters containing 26 structures, highest framenr is 25 [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (13 ms) [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 Analyzed 26 frames, last time 0.050 There are 8 clusters containing 26 structures, highest framenr is 25 [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (23 ms) [----------] 2 tests from ExtractClusterModuleTest (37 ms total) [----------] 2 tests from FreeVolumeModuleTest [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for CO2-RM. Set to zero. Could not determine VDW radius for 40 particles. These were set to zero. Reading frame 0 time 0.000 Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 cutoff = 0.18 nm probe_radius = 0 nm seed = 13 ninsert = 1000 probes per nm^3 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der Spoel and Luciano T. Costa Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View Environ. Sci. Technol. 47 (2013) pp. 7421-7429 -------- -------- --- Thank You --- -------- -------- Free volume 38.02 +/- 0.00 % Total volume 68.92 +/- 0.00 nm^3 Number of molecules 340 total mass 63491.38 Dalton Average molar mass: 186.74 Dalton Density rho: 1529.71 +/- 0.00 nm^3 Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 Fractional free volume 0.194 +/- 0.000 [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (47 ms) [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) Reading file ${WORKDIR}/gromacs-2022/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Reading frame 0 time 0.000 Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 cutoff = 0.18 nm probe_radius = 0 nm seed = 17 ninsert = 1000 probes per nm^3 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der Spoel and Luciano T. Costa Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View Environ. Sci. Technol. 47 (2013) pp. 7421-7429 -------- -------- --- Thank You --- -------- -------- Free volume 38.48 +/- 0.00 % Total volume 68.92 +/- 0.00 nm^3 Number of molecules 340 total mass 63491.38 Dalton Average molar mass: 186.74 Dalton Density rho: 1529.71 +/- 0.00 nm^3 Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 Fractional free volume 0.200 +/- 0.000 [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (45 ms) [----------] 2 tests from FreeVolumeModuleTest (93 ms total) [----------] 11 tests from MsdModuleTest [ RUN ] MsdModuleTest.threeDimensionalDiffusion Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 Analyzed 10 frames, last time 9.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] MsdModuleTest.threeDimensionalDiffusion (7 ms) [ RUN ] MsdModuleTest.twoDimensionalDiffusion Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 Analyzed 10 frames, last time 9.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] MsdModuleTest.twoDimensionalDiffusion (7 ms) [ RUN ] MsdModuleTest.oneDimensionalDiffusion Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 Analyzed 10 frames, last time 9.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] MsdModuleTest.oneDimensionalDiffusion (7 ms) [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 Analyzed 10 frames, last time 9.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (7 ms) [ RUN ] MsdModuleTest.multipleGroupsWork NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -558907891 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.multipleGroupsWork (29 ms) [ RUN ] MsdModuleTest.trestartLessThanDt NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -355033217 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.trestartLessThanDt (24 ms) [ RUN ] MsdModuleTest.trestartGreaterThanDt NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -1344541730 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.trestartGreaterThanDt (26 ms) [ RUN ] MsdModuleTest.molTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -23216131 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.molTest (25 ms) [ RUN ] MsdModuleTest.beginFit NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -453152257 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.beginFit (23 ms) [ RUN ] MsdModuleTest.endFit NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -134242562 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.endFit (23 ms) [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file alanine_vsite_solvated.top, line 28]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 1818.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: NVE simulation: will use the initial temperature of 288.764 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes NOTE: You provided an index file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx (with -n), but it was not used by any selection. Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022 (single precision) Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 Analyzed 21 frames, last time 40.000 Setting the LD random seed to -136448516 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' Excluding 2 bonded neighbours molecule type 'SOL' Cleaning up constraints and constant bonded interactions with virtual sites Converted 15 Bonds with virtual sites to connections, 7 left Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (23 ms) [----------] 11 tests from MsdModuleTest (205 ms total) [----------] 9 tests from PairDistanceModuleTest [ RUN ] PairDistanceModuleTest.ComputesAllDistances Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesAllDistances (5 ms) [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (5 ms) [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (5 ms) [ RUN ] PairDistanceModuleTest.ComputesMaxDistance Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesMaxDistance (5 ms) [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (5 ms) [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (5 ms) [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (5 ms) [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (5 ms) [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (6 ms) [----------] 9 tests from PairDistanceModuleTest (48 ms total) [----------] 5 tests from RdfModuleTest [ RUN ] RdfModuleTest.BasicTest Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] RdfModuleTest.BasicTest (18 ms) [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (13 ms) [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (18 ms) [ RUN ] RdfModuleTest.CalculatesSurf Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] RdfModuleTest.CalculatesSurf (11 ms) [ RUN ] RdfModuleTest.CalculatesXY Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] RdfModuleTest.CalculatesXY (19 ms) [----------] 5 tests from RdfModuleTest (82 ms total) [----------] 5 tests from SasaModuleTest [ RUN ] SasaModuleTest.BasicTest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 -------- -------- --- Thank You --- -------- -------- WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Analyzed topology coordinates [ OK ] SasaModuleTest.BasicTest (16 ms) [ RUN ] SasaModuleTest.HandlesSelectedResidues ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 -------- -------- --- Thank You --- -------- -------- WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Analyzed topology coordinates [ OK ] SasaModuleTest.HandlesSelectedResidues (10 ms) [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 -------- -------- --- Thank You --- -------- -------- WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Analyzed topology coordinates [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (8 ms) [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 -------- -------- --- Thank You --- -------- -------- WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Analyzed topology coordinates [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (11 ms) [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 -------- -------- --- Thank You --- -------- -------- WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Analyzed topology coordinates [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (11 ms) [----------] 5 tests from SasaModuleTest (58 ms total) [----------] 8 tests from SelectModuleTest [ RUN ] SelectModuleTest.BasicTest Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.BasicTest (9 ms) [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (6 ms) [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (6 ms) [ RUN ] SelectModuleTest.HandlesMaxPDBOutput Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.HandlesMaxPDBOutput (6 ms) [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (6 ms) [ RUN ] SelectModuleTest.NormalizesSizes Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.NormalizesSizes (3 ms) [ RUN ] SelectModuleTest.WritesResidueNumbers Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.WritesResidueNumbers (3 ms) [ RUN ] SelectModuleTest.WritesResidueIndices Analyzed topology coordinates WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] SelectModuleTest.WritesResidueIndices (3 ms) [----------] 8 tests from SelectModuleTest (45 ms total) [----------] 10 tests from SurfaceAreaTest [ RUN ] SurfaceAreaTest.ComputesSinglePoint [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) [ RUN ] SurfaceAreaTest.ComputesTwoPoints [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) [ RUN ] SurfaceAreaTest.SurfacePoints12 [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) [ RUN ] SurfaceAreaTest.SurfacePoints32 [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) [ RUN ] SurfaceAreaTest.SurfacePoints42 [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) [ RUN ] SurfaceAreaTest.SurfacePoints122 [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) [ RUN ] SurfaceAreaTest.Computes100Points [ OK ] SurfaceAreaTest.Computes100Points (0 ms) [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (2 ms) [----------] 10 tests from SurfaceAreaTest (9 ms total) [----------] 4 tests from TopologyInformation [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) [ RUN ] TopologyInformation.WorksWithGroFile WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TopologyInformation.WorksWithGroFile (3 ms) [ RUN ] TopologyInformation.WorksWithPdbFile WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TopologyInformation.WorksWithPdbFile (3 ms) [ RUN ] TopologyInformation.WorksWithTprFromPdbFile NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022 (single precision) Setting the LD random seed to -2232599 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data [ OK ] TopologyInformation.WorksWithTprFromPdbFile (138 ms) [----------] 4 tests from TopologyInformation (146 ms total) [----------] 4 tests from TrajectoryModuleTest [ RUN ] TrajectoryModuleTest.BasicTest Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryModuleTest.BasicTest (6 ms) [ RUN ] TrajectoryModuleTest.PlotsXOnly Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryModuleTest.PlotsXOnly (5 ms) [ RUN ] TrajectoryModuleTest.HandlesNoVelocities Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryModuleTest.HandlesNoVelocities (5 ms) [ RUN ] TrajectoryModuleTest.HandlesNoForces Reading frames from gro file 'Test system', 15 atoms. Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 Analyzed 2 frames, last time 0.000 WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Note, that this functionality may be removed in a future GROMACS version. Please, consider using another file format for your input. [ OK ] TrajectoryModuleTest.HandlesNoForces (5 ms) [----------] 4 tests from TrajectoryModuleTest (23 ms total) [----------] 5 tests from UnionFinderTest [ RUN ] UnionFinderTest.WorksEmpty [ OK ] UnionFinderTest.WorksEmpty (0 ms) [ RUN ] UnionFinderTest.BasicMerges [ OK ] UnionFinderTest.BasicMerges (0 ms) [ RUN ] UnionFinderTest.LargerMerges [ OK ] UnionFinderTest.LargerMerges (0 ms) [ RUN ] UnionFinderTest.LongRightMerge [ OK ] UnionFinderTest.LongRightMerge (0 ms) [ RUN ] UnionFinderTest.LongLeftMerge [ OK ] UnionFinderTest.LongLeftMerge (0 ms) [----------] 5 tests from UnionFinderTest (0 ms total) [----------] 1 test from MappedUnionFinderTest [ RUN ] MappedUnionFinderTest.BasicMerges [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) [----------] 1 test from MappedUnionFinderTest (0 ms total) [----------] Global test environment tear-down [==========] 96 tests from 17 test suites ran. (920 ms total) [ PASSED ] 96 tests. Test time = 1.59 sec ---------------------------------------------------------- Test Passed. "TrajectoryAnalysisUnitTests" end time: Feb 22 23:21 EST "TrajectoryAnalysisUnitTests" time elapsed: 00:00:01 ---------------------------------------------------------- 58/90 Testing: EnergyAnalysisUnitTests 58/90 Test: EnergyAnalysisUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/energyanalysis-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/EnergyAnalysisUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/energyanalysis/tests "EnergyAnalysisUnitTests" start time: Feb 22 23:21 EST Output: ---------------------------------------------------------- [==========] Running 7 tests from 4 test suites. [----------] Global test environment set-up. [----------] 1 test from DhdlTest [ RUN ] DhdlTest.ExtractDhdl Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file Reading file ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) Note: file tpx version 110, software tpx version 127 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 Wrote 8 lambda values with 101 samples as 808 dH data blocks to ${WORKDIR}/gromacs-2022/build/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg [ OK ] DhdlTest.ExtractDhdl (8 ms) [----------] 1 test from DhdlTest (9 ms total) [----------] 1 test from OriresTest [ RUN ] OriresTest.ExtractOrires Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file Reading file ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) Note: file tpx version 111, software tpx version 127 Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) End your selection with 0 Selecting all 7 orientation restraints Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 [ OK ] OriresTest.ExtractOrires (17 ms) [----------] 1 test from OriresTest (17 ms total) [----------] 3 tests from EnergyTest [ RUN ] EnergyTest.ExtractEnergy Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. ------------------------------------------------------------------- 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 13 Box-Z 14 Volume 15 Density 16 pV 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential -34142.2 39 228.993 -62.8906 (kJ/mol) Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) [ OK ] EnergyTest.ExtractEnergy (6 ms) [ RUN ] EnergyTest.ExtractEnergyByNumber Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. ------------------------------------------------------------------- 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 13 Box-Z 14 Volume 15 Density 16 pV 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) Pres. DC -268.49 3 8.52175 13.2804 (bar) [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) [ RUN ] EnergyTest.ExtractEnergyMixed Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. ------------------------------------------------------------------- 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 13 Box-Z 14 Volume 15 Density 16 pV 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) Pressure 5.34371 4.1 605.307 -4.88771 (bar) Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) Volume 25.0162 0.14 0.386769 0.598615 (nm^3) [ OK ] EnergyTest.ExtractEnergyMixed (5 ms) [----------] 3 tests from EnergyTest (16 ms total) [----------] 2 tests from ViscosityTest [ RUN ] ViscosityTest.EinsteinViscosity Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pres-XX 20.2092 65 717.193 185.978 (bar) Pres-XY -47.7351 39 372.522 207.456 (bar) Pres-XZ 11.477 31 379.79 6.80818 (bar) Pres-YX -47.7106 39 372.525 207.5 (bar) Pres-YY 38.9241 40 803.899 -27.1505 (bar) Pres-YZ -41.3534 45 401.216 114.663 (bar) Pres-ZX 11.5238 31 379.804 6.91707 (bar) Pres-ZY -41.3119 45 401.196 114.743 (bar) Pres-ZZ -43.1021 63 748.522 -173.491 (bar) Temperature 300.001 0.02 5.8425 -0.0130558 (K) Volume 25.0162 0.14 0.386769 0.598615 (nm^3) Pressure 5.34371 4.1 605.307 -4.88771 (bar) [ OK ] ViscosityTest.EinsteinViscosity (5573 ms) [ RUN ] ViscosityTest.EinsteinViscosityIntegral Opened ${WORKDIR}/gromacs-2022/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pres-XX 20.2092 65 717.193 185.978 (bar) Pres-XY -47.7351 39 372.522 207.456 (bar) Pres-XZ 11.477 31 379.79 6.80818 (bar) Pres-YX -47.7106 39 372.525 207.5 (bar) Pres-YY 38.9241 40 803.899 -27.1505 (bar) Pres-YZ -41.3534 45 401.216 114.663 (bar) Pres-ZX 11.5238 31 379.804 6.91707 (bar) Pres-ZY -41.3119 45 401.196 114.743 (bar) Pres-ZZ -43.1021 63 748.522 -173.491 (bar) Temperature 300.001 0.02 5.8425 -0.0130558 (K) Volume 25.0162 0.14 0.386769 0.598615 (nm^3) Pressure 5.34371 4.1 605.307 -4.88771 (bar) [ OK ] ViscosityTest.EinsteinViscosityIntegral (4799 ms) [----------] 2 tests from ViscosityTest (10372 ms total) [----------] Global test environment tear-down [==========] 7 tests from 4 test suites ran. (10416 ms total) [ PASSED ] 7 tests. Test time = 11.33 sec ---------------------------------------------------------- Test Passed. "EnergyAnalysisUnitTests" end time: Feb 22 23:22 EST "EnergyAnalysisUnitTests" time elapsed: 00:00:11 ---------------------------------------------------------- 59/90 Testing: ToolUnitTests 59/90 Test: ToolUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/tool-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/ToolUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests "ToolUnitTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 54 tests from 6 test suites. [----------] Global test environment set-up. [----------] 2 tests from DumpTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Setting the LD random seed to -1890717729 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data [ RUN ] DumpTest.WorksWithTpr Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022 (single precision) ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: inputrec: integrator = md tinit = 0 dt = 0.001 nsteps = 0 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1890717729 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = -1 rlist = 1.1 coulombtype = Cut-off coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 density-guided-simulation: active = false group = protein similarity-measure = inner-product atom-spreading-weight = unity force-constant = 1e+09 gaussian-transform-spreading-width = 0.2 gaussian-transform-spreading-range-in-multiples-of-width = 4 reference-density-filename = reference.mrc nst = 1 normalize-densities = true adaptive-force-scaling = false adaptive-force-scaling-time-constant = 4 shift-vector = transformation-matrix = qmmm-cp2k: active = false qmgroup = System qmmethod = PBE qmfilenames = qmcharge = 0 qmmultiplicity = 1 grpopts: nrdf: 465 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 header: bIr = present bBox = present bTop = present bX = present bV = present bF = not present natoms = 156 lambda = 0.000000e+00 buffer size = 59646 topology: name="First 10 residues from 1AKI" #atoms = 156 #molblock = 1 molblock (0): moltype = 0 "Protein_chain_B" #molecules = 1 #posres_xA = 0 #posres_xB = 0 bIntermolecularInteractions = false ffparams: atnr=10 ntypes=212 functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 reppow = 12 fudgeQQ = 0.5 cmap atomtypes: atomtype[ 0]={atomnumber= 7} atomtype[ 1]={atomnumber= 1} atomtype[ 2]={atomnumber= 6} atomtype[ 3]={atomnumber= 1} atomtype[ 4]={atomnumber= 6} atomtype[ 5]={atomnumber= 8} atomtype[ 6]={atomnumber= 6} atomtype[ 7]={atomnumber= 1} atomtype[ 8]={atomnumber= 6} atomtype[ 9]={atomnumber= 16} moltype (0): name="Protein_chain_B" atoms: atom (156): atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} atom (156): atom[0]={name="N"} atom[1]={name="H1"} atom[2]={name="H2"} atom[3]={name="H3"} atom[4]={name="CA"} atom[5]={name="HA"} atom[6]={name="CB"} atom[7]={name="HB1"} atom[8]={name="HB2"} atom[9]={name="CG"} atom[10]={name="HG1"} atom[11]={name="HG2"} atom[12]={name="CD"} atom[13]={name="HD1"} atom[14]={name="HD2"} atom[15]={name="CE"} atom[16]={name="HE1"} atom[17]={name="HE2"} atom[18]={name="NZ"} atom[19]={name="HZ1"} atom[20]={name="HZ2"} atom[21]={name="HZ3"} atom[22]={name="C"} atom[23]={name="O"} atom[24]={name="N"} atom[25]={name="H"} atom[26]={name="CA"} atom[27]={name="HA"} atom[28]={name="CB"} atom[29]={name="HB"} atom[30]={name="CG1"} atom[31]={name="HG11"} atom[32]={name="HG12"} atom[33]={name="HG13"} atom[34]={name="CG2"} atom[35]={name="HG21"} atom[36]={name="HG22"} atom[37]={name="HG23"} atom[38]={name="C"} atom[39]={name="O"} atom[40]={name="N"} atom[41]={name="H"} atom[42]={name="CA"} atom[43]={name="HA"} atom[44]={name="CB"} atom[45]={name="HB1"} atom[46]={name="HB2"} atom[47]={name="CG"} atom[48]={name="CD1"} atom[49]={name="HD1"} atom[50]={name="CD2"} atom[51]={name="HD2"} atom[52]={name="CE1"} atom[53]={name="HE1"} atom[54]={name="CE2"} atom[55]={name="HE2"} atom[56]={name="CZ"} atom[57]={name="HZ"} atom[58]={name="C"} atom[59]={name="O"} atom[60]={name="N"} atom[61]={name="H"} atom[62]={name="CA"} atom[63]={name="HA1"} atom[64]={name="HA2"} atom[65]={name="C"} atom[66]={name="O"} atom[67]={name="N"} atom[68]={name="H"} atom[69]={name="CA"} atom[70]={name="HA"} atom[71]={name="CB"} atom[72]={name="HB1"} atom[73]={name="HB2"} atom[74]={name="CG"} atom[75]={name="HG1"} atom[76]={name="HG2"} atom[77]={name="CD"} atom[78]={name="HD1"} atom[79]={name="HD2"} atom[80]={name="NE"} atom[81]={name="HE"} atom[82]={name="CZ"} atom[83]={name="NH1"} atom[84]={name="HH11"} atom[85]={name="HH12"} atom[86]={name="NH2"} atom[87]={name="HH21"} atom[88]={name="HH22"} atom[89]={name="C"} atom[90]={name="O"} atom[91]={name="N"} atom[92]={name="H"} atom[93]={name="CA"} atom[94]={name="HA"} atom[95]={name="CB"} atom[96]={name="HB1"} atom[97]={name="HB2"} atom[98]={name="SG"} atom[99]={name="HG"} atom[100]={name="C"} atom[101]={name="O"} atom[102]={name="N"} atom[103]={name="H"} atom[104]={name="CA"} atom[105]={name="HA"} atom[106]={name="CB"} atom[107]={name="HB1"} atom[108]={name="HB2"} atom[109]={name="CG"} atom[110]={name="HG1"} atom[111]={name="HG2"} atom[112]={name="CD"} atom[113]={name="OE1"} atom[114]={name="OE2"} atom[115]={name="C"} atom[116]={name="O"} atom[117]={name="N"} atom[118]={name="H"} atom[119]={name="CA"} atom[120]={name="HA"} atom[121]={name="CB"} atom[122]={name="HB1"} atom[123]={name="HB2"} atom[124]={name="CG"} atom[125]={name="HG"} atom[126]={name="CD1"} atom[127]={name="HD11"} atom[128]={name="HD12"} atom[129]={name="HD13"} atom[130]={name="CD2"} atom[131]={name="HD21"} atom[132]={name="HD22"} atom[133]={name="HD23"} atom[134]={name="C"} atom[135]={name="O"} atom[136]={name="N"} atom[137]={name="H"} atom[138]={name="CA"} atom[139]={name="HA"} atom[140]={name="CB"} atom[141]={name="HB1"} atom[142]={name="HB2"} atom[143]={name="HB3"} atom[144]={name="C"} atom[145]={name="O"} atom[146]={name="N"} atom[147]={name="H"} atom[148]={name="CA"} atom[149]={name="HA"} atom[150]={name="CB"} atom[151]={name="HB1"} atom[152]={name="HB2"} atom[153]={name="HB3"} atom[154]={name="C"} atom[155]={name="O"} type (156): type[0]={name="opls_287",nameB="opls_287"} type[1]={name="opls_290",nameB="opls_290"} type[2]={name="opls_290",nameB="opls_290"} type[3]={name="opls_290",nameB="opls_290"} type[4]={name="opls_293B",nameB="opls_293B"} type[5]={name="opls_140",nameB="opls_140"} type[6]={name="opls_136",nameB="opls_136"} type[7]={name="opls_140",nameB="opls_140"} type[8]={name="opls_140",nameB="opls_140"} type[9]={name="opls_136",nameB="opls_136"} type[10]={name="opls_140",nameB="opls_140"} type[11]={name="opls_140",nameB="opls_140"} type[12]={name="opls_136",nameB="opls_136"} type[13]={name="opls_140",nameB="opls_140"} type[14]={name="opls_140",nameB="opls_140"} type[15]={name="opls_292",nameB="opls_292"} type[16]={name="opls_140",nameB="opls_140"} type[17]={name="opls_140",nameB="opls_140"} type[18]={name="opls_287",nameB="opls_287"} type[19]={name="opls_290",nameB="opls_290"} type[20]={name="opls_290",nameB="opls_290"} type[21]={name="opls_290",nameB="opls_290"} type[22]={name="opls_235",nameB="opls_235"} type[23]={name="opls_236",nameB="opls_236"} type[24]={name="opls_238",nameB="opls_238"} type[25]={name="opls_241",nameB="opls_241"} type[26]={name="opls_224B",nameB="opls_224B"} type[27]={name="opls_140",nameB="opls_140"} type[28]={name="opls_137",nameB="opls_137"} type[29]={name="opls_140",nameB="opls_140"} type[30]={name="opls_135",nameB="opls_135"} type[31]={name="opls_140",nameB="opls_140"} type[32]={name="opls_140",nameB="opls_140"} type[33]={name="opls_140",nameB="opls_140"} type[34]={name="opls_135",nameB="opls_135"} type[35]={name="opls_140",nameB="opls_140"} type[36]={name="opls_140",nameB="opls_140"} type[37]={name="opls_140",nameB="opls_140"} type[38]={name="opls_235",nameB="opls_235"} type[39]={name="opls_236",nameB="opls_236"} type[40]={name="opls_238",nameB="opls_238"} type[41]={name="opls_241",nameB="opls_241"} type[42]={name="opls_224B",nameB="opls_224B"} type[43]={name="opls_140",nameB="opls_140"} type[44]={name="opls_149",nameB="opls_149"} type[45]={name="opls_140",nameB="opls_140"} type[46]={name="opls_140",nameB="opls_140"} type[47]={name="opls_145",nameB="opls_145"} type[48]={name="opls_145",nameB="opls_145"} type[49]={name="opls_146",nameB="opls_146"} type[50]={name="opls_145",nameB="opls_145"} type[51]={name="opls_146",nameB="opls_146"} type[52]={name="opls_145",nameB="opls_145"} type[53]={name="opls_146",nameB="opls_146"} type[54]={name="opls_145",nameB="opls_145"} type[55]={name="opls_146",nameB="opls_146"} type[56]={name="opls_145",nameB="opls_145"} type[57]={name="opls_146",nameB="opls_146"} type[58]={name="opls_235",nameB="opls_235"} type[59]={name="opls_236",nameB="opls_236"} type[60]={name="opls_238",nameB="opls_238"} type[61]={name="opls_241",nameB="opls_241"} type[62]={name="opls_223B",nameB="opls_223B"} type[63]={name="opls_140",nameB="opls_140"} type[64]={name="opls_140",nameB="opls_140"} type[65]={name="opls_235",nameB="opls_235"} type[66]={name="opls_236",nameB="opls_236"} type[67]={name="opls_238",nameB="opls_238"} type[68]={name="opls_241",nameB="opls_241"} type[69]={name="opls_224B",nameB="opls_224B"} type[70]={name="opls_140",nameB="opls_140"} type[71]={name="opls_136",nameB="opls_136"} type[72]={name="opls_140",nameB="opls_140"} type[73]={name="opls_140",nameB="opls_140"} type[74]={name="opls_308",nameB="opls_308"} type[75]={name="opls_140",nameB="opls_140"} type[76]={name="opls_140",nameB="opls_140"} type[77]={name="opls_307",nameB="opls_307"} type[78]={name="opls_140",nameB="opls_140"} type[79]={name="opls_140",nameB="opls_140"} type[80]={name="opls_303",nameB="opls_303"} type[81]={name="opls_304",nameB="opls_304"} type[82]={name="opls_302",nameB="opls_302"} type[83]={name="opls_300",nameB="opls_300"} type[84]={name="opls_301",nameB="opls_301"} type[85]={name="opls_301",nameB="opls_301"} type[86]={name="opls_300",nameB="opls_300"} type[87]={name="opls_301",nameB="opls_301"} type[88]={name="opls_301",nameB="opls_301"} type[89]={name="opls_235",nameB="opls_235"} type[90]={name="opls_236",nameB="opls_236"} type[91]={name="opls_238",nameB="opls_238"} type[92]={name="opls_241",nameB="opls_241"} type[93]={name="opls_224B",nameB="opls_224B"} type[94]={name="opls_140",nameB="opls_140"} type[95]={name="opls_206",nameB="opls_206"} type[96]={name="opls_140",nameB="opls_140"} type[97]={name="opls_140",nameB="opls_140"} type[98]={name="opls_200",nameB="opls_200"} type[99]={name="opls_204",nameB="opls_204"} type[100]={name="opls_235",nameB="opls_235"} type[101]={name="opls_236",nameB="opls_236"} type[102]={name="opls_238",nameB="opls_238"} type[103]={name="opls_241",nameB="opls_241"} type[104]={name="opls_224B",nameB="opls_224B"} type[105]={name="opls_140",nameB="opls_140"} type[106]={name="opls_136",nameB="opls_136"} type[107]={name="opls_140",nameB="opls_140"} type[108]={name="opls_140",nameB="opls_140"} type[109]={name="opls_274",nameB="opls_274"} type[110]={name="opls_140",nameB="opls_140"} type[111]={name="opls_140",nameB="opls_140"} type[112]={name="opls_271",nameB="opls_271"} type[113]={name="opls_272",nameB="opls_272"} type[114]={name="opls_272",nameB="opls_272"} type[115]={name="opls_235",nameB="opls_235"} type[116]={name="opls_236",nameB="opls_236"} type[117]={name="opls_238",nameB="opls_238"} type[118]={name="opls_241",nameB="opls_241"} type[119]={name="opls_224B",nameB="opls_224B"} type[120]={name="opls_140",nameB="opls_140"} type[121]={name="opls_136",nameB="opls_136"} type[122]={name="opls_140",nameB="opls_140"} type[123]={name="opls_140",nameB="opls_140"} type[124]={name="opls_137",nameB="opls_137"} type[125]={name="opls_140",nameB="opls_140"} type[126]={name="opls_135",nameB="opls_135"} type[127]={name="opls_140",nameB="opls_140"} type[128]={name="opls_140",nameB="opls_140"} type[129]={name="opls_140",nameB="opls_140"} type[130]={name="opls_135",nameB="opls_135"} type[131]={name="opls_140",nameB="opls_140"} type[132]={name="opls_140",nameB="opls_140"} type[133]={name="opls_140",nameB="opls_140"} type[134]={name="opls_235",nameB="opls_235"} type[135]={name="opls_236",nameB="opls_236"} type[136]={name="opls_238",nameB="opls_238"} type[137]={name="opls_241",nameB="opls_241"} type[138]={name="opls_224B",nameB="opls_224B"} type[139]={name="opls_140",nameB="opls_140"} type[140]={name="opls_135",nameB="opls_135"} type[141]={name="opls_140",nameB="opls_140"} type[142]={name="opls_140",nameB="opls_140"} type[143]={name="opls_140",nameB="opls_140"} type[144]={name="opls_235",nameB="opls_235"} type[145]={name="opls_236",nameB="opls_236"} type[146]={name="opls_238",nameB="opls_238"} type[147]={name="opls_241",nameB="opls_241"} type[148]={name="opls_224B",nameB="opls_224B"} type[149]={name="opls_140",nameB="opls_140"} type[150]={name="opls_135",nameB="opls_135"} type[151]={name="opls_140",nameB="opls_140"} type[152]={name="opls_140",nameB="opls_140"} type[153]={name="opls_140",nameB="opls_140"} type[154]={name="opls_235",nameB="opls_235"} type[155]={name="opls_236",nameB="opls_236"} residue (10): residue[0]={name="LYS", nr=1, ic=' '} residue[1]={name="VAL", nr=2, ic=' '} residue[2]={name="PHE", nr=3, ic=' '} residue[3]={name="GLY", nr=4, ic=' '} residue[4]={name="ARG", nr=5, ic=' '} residue[5]={name="CYS", nr=6, ic=' '} residue[6]={name="GLU", nr=7, ic=' '} residue[7]={name="LEU", nr=8, ic=' '} residue[8]={name="ALA", nr=9, ic=' '} residue[9]={name="ALA", nr=10, ic=' '} excls: numLists=156 numElements=1828 excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26} excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24} excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22} excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 38} excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 40} excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 40} excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40} excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38} excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38} excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38} excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 40, 41, 42, 43, 44, 58} excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60} excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 58, 59, 60, 61, 62} excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60} excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 58, 59, 60} excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58} excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57} excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57} excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63, 64, 65} excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67} excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69} excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 89} excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 91} excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89, 90, 91, 92, 93} excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 91} excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 89, 90, 91} excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 89} excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 86} excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88} excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88} excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} excls[84][num=6]={80, 82, 83, 84, 85, 86} excls[85][num=6]={80, 82, 83, 84, 85, 86} excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} excls[87][num=6]={80, 82, 83, 86, 87, 88} excls[88][num=6]={80, 82, 83, 86, 87, 88} excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 91, 92, 93, 94, 95, 100} excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 102} excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104} excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 102} excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102} excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} excls[99][num=6]={93, 95, 96, 97, 98, 99} excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 102, 103, 104, 105, 106, 115} excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 115, 116, 117} excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 115, 116, 117} excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117} excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 112, 115} excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 112, 115} excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115} excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 114} excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 114} excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 114} excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 115, 116, 117, 118, 119, 120, 121, 134} excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 134, 135, 136} excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 134, 135, 136} excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 130, 134} excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 130, 134} excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134} excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133} excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133} excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133} excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 134, 135, 136, 137, 138, 139, 140, 144} excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146} excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148} excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146} excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146} excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 154} excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155} excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155} excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155} excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155} excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155} excls[155][num=6]={146, 148, 149, 150, 154, 155} Bond: nr: 468 iatoms: 0 type=100 (BONDS) 0 1 1 type=100 (BONDS) 0 2 2 type=100 (BONDS) 0 3 3 type=101 (BONDS) 0 4 4 type=102 (BONDS) 4 5 5 type=103 (BONDS) 4 6 6 type=104 (BONDS) 4 22 7 type=102 (BONDS) 6 7 8 type=102 (BONDS) 6 8 9 type=103 (BONDS) 6 9 10 type=102 (BONDS) 9 10 11 type=102 (BONDS) 9 11 12 type=103 (BONDS) 9 12 13 type=102 (BONDS) 12 13 14 type=102 (BONDS) 12 14 15 type=103 (BONDS) 12 15 16 type=102 (BONDS) 15 16 17 type=102 (BONDS) 15 17 18 type=101 (BONDS) 15 18 19 type=100 (BONDS) 18 19 20 type=100 (BONDS) 18 20 21 type=100 (BONDS) 18 21 22 type=105 (BONDS) 22 23 23 type=106 (BONDS) 22 24 24 type=100 (BONDS) 24 25 25 type=107 (BONDS) 24 26 26 type=102 (BONDS) 26 27 27 type=103 (BONDS) 26 28 28 type=104 (BONDS) 26 38 29 type=102 (BONDS) 28 29 30 type=103 (BONDS) 28 30 31 type=103 (BONDS) 28 34 32 type=102 (BONDS) 30 31 33 type=102 (BONDS) 30 32 34 type=102 (BONDS) 30 33 35 type=102 (BONDS) 34 35 36 type=102 (BONDS) 34 36 37 type=102 (BONDS) 34 37 38 type=105 (BONDS) 38 39 39 type=106 (BONDS) 38 40 40 type=100 (BONDS) 40 41 41 type=107 (BONDS) 40 42 42 type=102 (BONDS) 42 43 43 type=103 (BONDS) 42 44 44 type=104 (BONDS) 42 58 45 type=102 (BONDS) 44 45 46 type=102 (BONDS) 44 46 47 type=108 (BONDS) 44 47 48 type=109 (BONDS) 47 48 49 type=109 (BONDS) 47 50 50 type=110 (BONDS) 48 49 51 type=109 (BONDS) 48 52 52 type=110 (BONDS) 50 51 53 type=109 (BONDS) 50 54 54 type=110 (BONDS) 52 53 55 type=109 (BONDS) 52 56 56 type=110 (BONDS) 54 55 57 type=109 (BONDS) 54 56 58 type=110 (BONDS) 56 57 59 type=105 (BONDS) 58 59 60 type=106 (BONDS) 58 60 61 type=100 (BONDS) 60 61 62 type=107 (BONDS) 60 62 63 type=102 (BONDS) 62 63 64 type=102 (BONDS) 62 64 65 type=104 (BONDS) 62 65 66 type=105 (BONDS) 65 66 67 type=106 (BONDS) 65 67 68 type=100 (BONDS) 67 68 69 type=107 (BONDS) 67 69 70 type=102 (BONDS) 69 70 71 type=103 (BONDS) 69 71 72 type=104 (BONDS) 69 89 73 type=102 (BONDS) 71 72 74 type=102 (BONDS) 71 73 75 type=103 (BONDS) 71 74 76 type=102 (BONDS) 74 75 77 type=102 (BONDS) 74 76 78 type=103 (BONDS) 74 77 79 type=102 (BONDS) 77 78 80 type=102 (BONDS) 77 79 81 type=111 (BONDS) 77 80 82 type=100 (BONDS) 80 81 83 type=112 (BONDS) 80 82 84 type=112 (BONDS) 82 83 85 type=112 (BONDS) 82 86 86 type=100 (BONDS) 83 84 87 type=100 (BONDS) 83 85 88 type=100 (BONDS) 86 87 89 type=100 (BONDS) 86 88 90 type=105 (BONDS) 89 90 91 type=106 (BONDS) 89 91 92 type=100 (BONDS) 91 92 93 type=107 (BONDS) 91 93 94 type=102 (BONDS) 93 94 95 type=103 (BONDS) 93 95 96 type=104 (BONDS) 93 100 97 type=102 (BONDS) 95 96 98 type=102 (BONDS) 95 97 99 type=113 (BONDS) 95 98 100 type=114 (BONDS) 98 99 101 type=105 (BONDS) 100 101 102 type=106 (BONDS) 100 102 103 type=100 (BONDS) 102 103 104 type=107 (BONDS) 102 104 105 type=102 (BONDS) 104 105 106 type=103 (BONDS) 104 106 107 type=104 (BONDS) 104 115 108 type=102 (BONDS) 106 107 109 type=102 (BONDS) 106 108 110 type=103 (BONDS) 106 109 111 type=102 (BONDS) 109 110 112 type=102 (BONDS) 109 111 113 type=104 (BONDS) 109 112 114 type=115 (BONDS) 112 113 115 type=115 (BONDS) 112 114 116 type=105 (BONDS) 115 116 117 type=106 (BONDS) 115 117 118 type=100 (BONDS) 117 118 119 type=107 (BONDS) 117 119 120 type=102 (BONDS) 119 120 121 type=103 (BONDS) 119 121 122 type=104 (BONDS) 119 134 123 type=102 (BONDS) 121 122 124 type=102 (BONDS) 121 123 125 type=103 (BONDS) 121 124 126 type=102 (BONDS) 124 125 127 type=103 (BONDS) 124 126 128 type=103 (BONDS) 124 130 129 type=102 (BONDS) 126 127 130 type=102 (BONDS) 126 128 131 type=102 (BONDS) 126 129 132 type=102 (BONDS) 130 131 133 type=102 (BONDS) 130 132 134 type=102 (BONDS) 130 133 135 type=105 (BONDS) 134 135 136 type=106 (BONDS) 134 136 137 type=100 (BONDS) 136 137 138 type=107 (BONDS) 136 138 139 type=102 (BONDS) 138 139 140 type=103 (BONDS) 138 140 141 type=104 (BONDS) 138 144 142 type=102 (BONDS) 140 141 143 type=102 (BONDS) 140 142 144 type=102 (BONDS) 140 143 145 type=105 (BONDS) 144 145 146 type=106 (BONDS) 144 146 147 type=100 (BONDS) 146 147 148 type=107 (BONDS) 146 148 149 type=102 (BONDS) 148 149 150 type=103 (BONDS) 148 150 151 type=104 (BONDS) 148 154 152 type=102 (BONDS) 150 151 153 type=102 (BONDS) 150 152 154 type=102 (BONDS) 150 153 155 type=105 (BONDS) 154 155 G96Bond: nr: 0 Morse: nr: 0 Cubic Bonds: nr: 0 Connect Bonds: nr: 0 Harmonic Pot.: nr: 0 FENE Bonds: nr: 0 Tab. Bonds: nr: 0 Tab. Bonds NC: nr: 0 Restraint Pot.: nr: 0 Angle: nr: 1124 iatoms: 0 type=116 (ANGLES) 1 0 2 1 type=116 (ANGLES) 1 0 3 2 type=116 (ANGLES) 1 0 4 3 type=116 (ANGLES) 2 0 3 4 type=116 (ANGLES) 2 0 4 5 type=116 (ANGLES) 3 0 4 6 type=116 (ANGLES) 0 4 5 7 type=117 (ANGLES) 0 4 6 8 type=117 (ANGLES) 0 4 22 9 type=118 (ANGLES) 5 4 6 10 type=116 (ANGLES) 5 4 22 11 type=119 (ANGLES) 6 4 22 12 type=118 (ANGLES) 4 6 7 13 type=118 (ANGLES) 4 6 8 14 type=120 (ANGLES) 4 6 9 15 type=121 (ANGLES) 7 6 8 16 type=118 (ANGLES) 7 6 9 17 type=118 (ANGLES) 8 6 9 18 type=118 (ANGLES) 6 9 10 19 type=118 (ANGLES) 6 9 11 20 type=120 (ANGLES) 6 9 12 21 type=121 (ANGLES) 10 9 11 22 type=118 (ANGLES) 10 9 12 23 type=118 (ANGLES) 11 9 12 24 type=118 (ANGLES) 9 12 13 25 type=118 (ANGLES) 9 12 14 26 type=120 (ANGLES) 9 12 15 27 type=121 (ANGLES) 13 12 14 28 type=118 (ANGLES) 13 12 15 29 type=118 (ANGLES) 14 12 15 30 type=118 (ANGLES) 12 15 16 31 type=118 (ANGLES) 12 15 17 32 type=117 (ANGLES) 12 15 18 33 type=121 (ANGLES) 16 15 17 34 type=116 (ANGLES) 16 15 18 35 type=116 (ANGLES) 17 15 18 36 type=116 (ANGLES) 15 18 19 37 type=116 (ANGLES) 15 18 20 38 type=116 (ANGLES) 15 18 21 39 type=116 (ANGLES) 19 18 20 40 type=116 (ANGLES) 19 18 21 41 type=116 (ANGLES) 20 18 21 42 type=122 (ANGLES) 4 22 23 43 type=123 (ANGLES) 4 22 24 44 type=124 (ANGLES) 23 22 24 45 type=125 (ANGLES) 22 24 25 46 type=126 (ANGLES) 22 24 26 47 type=127 (ANGLES) 25 24 26 48 type=116 (ANGLES) 24 26 27 49 type=128 (ANGLES) 24 26 28 50 type=129 (ANGLES) 24 26 38 51 type=118 (ANGLES) 27 26 28 52 type=116 (ANGLES) 27 26 38 53 type=119 (ANGLES) 28 26 38 54 type=118 (ANGLES) 26 28 29 55 type=120 (ANGLES) 26 28 30 56 type=120 (ANGLES) 26 28 34 57 type=118 (ANGLES) 29 28 30 58 type=118 (ANGLES) 29 28 34 59 type=120 (ANGLES) 30 28 34 60 type=118 (ANGLES) 28 30 31 61 type=118 (ANGLES) 28 30 32 62 type=118 (ANGLES) 28 30 33 63 type=121 (ANGLES) 31 30 32 64 type=121 (ANGLES) 31 30 33 65 type=121 (ANGLES) 32 30 33 66 type=118 (ANGLES) 28 34 35 67 type=118 (ANGLES) 28 34 36 68 type=118 (ANGLES) 28 34 37 69 type=121 (ANGLES) 35 34 36 70 type=121 (ANGLES) 35 34 37 71 type=121 (ANGLES) 36 34 37 72 type=122 (ANGLES) 26 38 39 73 type=123 (ANGLES) 26 38 40 74 type=124 (ANGLES) 39 38 40 75 type=125 (ANGLES) 38 40 41 76 type=126 (ANGLES) 38 40 42 77 type=127 (ANGLES) 41 40 42 78 type=116 (ANGLES) 40 42 43 79 type=128 (ANGLES) 40 42 44 80 type=129 (ANGLES) 40 42 58 81 type=118 (ANGLES) 43 42 44 82 type=116 (ANGLES) 43 42 58 83 type=119 (ANGLES) 44 42 58 84 type=118 (ANGLES) 42 44 45 85 type=118 (ANGLES) 42 44 46 86 type=130 (ANGLES) 42 44 47 87 type=121 (ANGLES) 45 44 46 88 type=116 (ANGLES) 45 44 47 89 type=116 (ANGLES) 46 44 47 90 type=131 (ANGLES) 44 47 48 91 type=131 (ANGLES) 44 47 50 92 type=132 (ANGLES) 48 47 50 93 type=133 (ANGLES) 47 48 49 94 type=132 (ANGLES) 47 48 52 95 type=133 (ANGLES) 49 48 52 96 type=133 (ANGLES) 47 50 51 97 type=132 (ANGLES) 47 50 54 98 type=133 (ANGLES) 51 50 54 99 type=133 (ANGLES) 48 52 53 100 type=132 (ANGLES) 48 52 56 101 type=133 (ANGLES) 53 52 56 102 type=133 (ANGLES) 50 54 55 103 type=132 (ANGLES) 50 54 56 104 type=133 (ANGLES) 55 54 56 105 type=132 (ANGLES) 52 56 54 106 type=133 (ANGLES) 52 56 57 107 type=133 (ANGLES) 54 56 57 108 type=122 (ANGLES) 42 58 59 109 type=123 (ANGLES) 42 58 60 110 type=124 (ANGLES) 59 58 60 111 type=125 (ANGLES) 58 60 61 112 type=126 (ANGLES) 58 60 62 113 type=127 (ANGLES) 61 60 62 114 type=116 (ANGLES) 60 62 63 115 type=116 (ANGLES) 60 62 64 116 type=129 (ANGLES) 60 62 65 117 type=121 (ANGLES) 63 62 64 118 type=116 (ANGLES) 63 62 65 119 type=116 (ANGLES) 64 62 65 120 type=122 (ANGLES) 62 65 66 121 type=123 (ANGLES) 62 65 67 122 type=124 (ANGLES) 66 65 67 123 type=125 (ANGLES) 65 67 68 124 type=126 (ANGLES) 65 67 69 125 type=127 (ANGLES) 68 67 69 126 type=116 (ANGLES) 67 69 70 127 type=128 (ANGLES) 67 69 71 128 type=129 (ANGLES) 67 69 89 129 type=118 (ANGLES) 70 69 71 130 type=116 (ANGLES) 70 69 89 131 type=119 (ANGLES) 71 69 89 132 type=118 (ANGLES) 69 71 72 133 type=118 (ANGLES) 69 71 73 134 type=120 (ANGLES) 69 71 74 135 type=121 (ANGLES) 72 71 73 136 type=118 (ANGLES) 72 71 74 137 type=118 (ANGLES) 73 71 74 138 type=118 (ANGLES) 71 74 75 139 type=118 (ANGLES) 71 74 76 140 type=120 (ANGLES) 71 74 77 141 type=121 (ANGLES) 75 74 76 142 type=118 (ANGLES) 75 74 77 143 type=118 (ANGLES) 76 74 77 144 type=118 (ANGLES) 74 77 78 145 type=118 (ANGLES) 74 77 79 146 type=117 (ANGLES) 74 77 80 147 type=121 (ANGLES) 78 77 79 148 type=116 (ANGLES) 78 77 80 149 type=116 (ANGLES) 79 77 80 150 type=134 (ANGLES) 77 80 81 151 type=135 (ANGLES) 77 80 82 152 type=133 (ANGLES) 81 80 82 153 type=131 (ANGLES) 80 82 83 154 type=131 (ANGLES) 80 82 86 155 type=131 (ANGLES) 83 82 86 156 type=133 (ANGLES) 82 83 84 157 type=133 (ANGLES) 82 83 85 158 type=133 (ANGLES) 84 83 85 159 type=133 (ANGLES) 82 86 87 160 type=133 (ANGLES) 82 86 88 161 type=133 (ANGLES) 87 86 88 162 type=122 (ANGLES) 69 89 90 163 type=123 (ANGLES) 69 89 91 164 type=124 (ANGLES) 90 89 91 165 type=125 (ANGLES) 89 91 92 166 type=126 (ANGLES) 89 91 93 167 type=127 (ANGLES) 92 91 93 168 type=116 (ANGLES) 91 93 94 169 type=128 (ANGLES) 91 93 95 170 type=129 (ANGLES) 91 93 100 171 type=118 (ANGLES) 94 93 95 172 type=116 (ANGLES) 94 93 100 173 type=119 (ANGLES) 95 93 100 174 type=118 (ANGLES) 93 95 96 175 type=118 (ANGLES) 93 95 97 176 type=136 (ANGLES) 93 95 98 177 type=121 (ANGLES) 96 95 97 178 type=116 (ANGLES) 96 95 98 179 type=116 (ANGLES) 97 95 98 180 type=137 (ANGLES) 95 98 99 181 type=122 (ANGLES) 93 100 101 182 type=123 (ANGLES) 93 100 102 183 type=124 (ANGLES) 101 100 102 184 type=125 (ANGLES) 100 102 103 185 type=126 (ANGLES) 100 102 104 186 type=127 (ANGLES) 103 102 104 187 type=116 (ANGLES) 102 104 105 188 type=128 (ANGLES) 102 104 106 189 type=129 (ANGLES) 102 104 115 190 type=118 (ANGLES) 105 104 106 191 type=116 (ANGLES) 105 104 115 192 type=119 (ANGLES) 106 104 115 193 type=118 (ANGLES) 104 106 107 194 type=118 (ANGLES) 104 106 108 195 type=120 (ANGLES) 104 106 109 196 type=121 (ANGLES) 107 106 108 197 type=118 (ANGLES) 107 106 109 198 type=118 (ANGLES) 108 106 109 199 type=118 (ANGLES) 106 109 110 200 type=118 (ANGLES) 106 109 111 201 type=119 (ANGLES) 106 109 112 202 type=121 (ANGLES) 110 109 111 203 type=116 (ANGLES) 110 109 112 204 type=116 (ANGLES) 111 109 112 205 type=138 (ANGLES) 109 112 113 206 type=138 (ANGLES) 109 112 114 207 type=139 (ANGLES) 113 112 114 208 type=122 (ANGLES) 104 115 116 209 type=123 (ANGLES) 104 115 117 210 type=124 (ANGLES) 116 115 117 211 type=125 (ANGLES) 115 117 118 212 type=126 (ANGLES) 115 117 119 213 type=127 (ANGLES) 118 117 119 214 type=116 (ANGLES) 117 119 120 215 type=128 (ANGLES) 117 119 121 216 type=129 (ANGLES) 117 119 134 217 type=118 (ANGLES) 120 119 121 218 type=116 (ANGLES) 120 119 134 219 type=119 (ANGLES) 121 119 134 220 type=118 (ANGLES) 119 121 122 221 type=118 (ANGLES) 119 121 123 222 type=120 (ANGLES) 119 121 124 223 type=121 (ANGLES) 122 121 123 224 type=118 (ANGLES) 122 121 124 225 type=118 (ANGLES) 123 121 124 226 type=118 (ANGLES) 121 124 125 227 type=120 (ANGLES) 121 124 126 228 type=120 (ANGLES) 121 124 130 229 type=118 (ANGLES) 125 124 126 230 type=118 (ANGLES) 125 124 130 231 type=120 (ANGLES) 126 124 130 232 type=118 (ANGLES) 124 126 127 233 type=118 (ANGLES) 124 126 128 234 type=118 (ANGLES) 124 126 129 235 type=121 (ANGLES) 127 126 128 236 type=121 (ANGLES) 127 126 129 237 type=121 (ANGLES) 128 126 129 238 type=118 (ANGLES) 124 130 131 239 type=118 (ANGLES) 124 130 132 240 type=118 (ANGLES) 124 130 133 241 type=121 (ANGLES) 131 130 132 242 type=121 (ANGLES) 131 130 133 243 type=121 (ANGLES) 132 130 133 244 type=122 (ANGLES) 119 134 135 245 type=123 (ANGLES) 119 134 136 246 type=124 (ANGLES) 135 134 136 247 type=125 (ANGLES) 134 136 137 248 type=126 (ANGLES) 134 136 138 249 type=127 (ANGLES) 137 136 138 250 type=116 (ANGLES) 136 138 139 251 type=128 (ANGLES) 136 138 140 252 type=129 (ANGLES) 136 138 144 253 type=118 (ANGLES) 139 138 140 254 type=116 (ANGLES) 139 138 144 255 type=119 (ANGLES) 140 138 144 256 type=118 (ANGLES) 138 140 141 257 type=118 (ANGLES) 138 140 142 258 type=118 (ANGLES) 138 140 143 259 type=121 (ANGLES) 141 140 142 260 type=121 (ANGLES) 141 140 143 261 type=121 (ANGLES) 142 140 143 262 type=122 (ANGLES) 138 144 145 263 type=123 (ANGLES) 138 144 146 264 type=124 (ANGLES) 145 144 146 265 type=125 (ANGLES) 144 146 147 266 type=126 (ANGLES) 144 146 148 267 type=127 (ANGLES) 147 146 148 268 type=116 (ANGLES) 146 148 149 269 type=128 (ANGLES) 146 148 150 270 type=129 (ANGLES) 146 148 154 271 type=118 (ANGLES) 149 148 150 272 type=116 (ANGLES) 149 148 154 273 type=119 (ANGLES) 150 148 154 274 type=118 (ANGLES) 148 150 151 275 type=118 (ANGLES) 148 150 152 276 type=118 (ANGLES) 148 150 153 277 type=121 (ANGLES) 151 150 152 278 type=121 (ANGLES) 151 150 153 279 type=121 (ANGLES) 152 150 153 280 type=122 (ANGLES) 148 154 155 G96Angle: nr: 0 Restricted Angles: nr: 0 Lin. Angle: nr: 0 Bond-Cross: nr: 0 BA-Cross: nr: 0 U-B: nr: 0 Quartic Angles: nr: 0 Tab. Angles: nr: 0 Proper Dih.: nr: 145 iatoms: 0 type=140 (PDIHS) 4 24 22 23 1 type=141 (PDIHS) 22 26 24 25 2 type=140 (PDIHS) 26 40 38 39 3 type=141 (PDIHS) 38 42 40 41 4 type=140 (PDIHS) 42 60 58 59 5 type=142 (PDIHS) 44 47 50 48 6 type=142 (PDIHS) 47 52 48 49 7 type=142 (PDIHS) 47 54 50 51 8 type=142 (PDIHS) 48 56 52 53 9 type=142 (PDIHS) 50 56 54 55 10 type=142 (PDIHS) 52 54 56 57 11 type=141 (PDIHS) 58 62 60 61 12 type=140 (PDIHS) 62 67 65 66 13 type=141 (PDIHS) 65 69 67 68 14 type=140 (PDIHS) 69 91 89 90 15 type=141 (PDIHS) 77 82 80 81 16 type=140 (PDIHS) 80 83 82 86 17 type=141 (PDIHS) 82 84 83 85 18 type=141 (PDIHS) 82 87 86 88 19 type=141 (PDIHS) 89 93 91 92 20 type=140 (PDIHS) 93 102 100 101 21 type=141 (PDIHS) 100 104 102 103 22 type=140 (PDIHS) 104 117 115 116 23 type=140 (PDIHS) 109 113 112 114 24 type=141 (PDIHS) 115 119 117 118 25 type=140 (PDIHS) 119 136 134 135 26 type=141 (PDIHS) 134 138 136 137 27 type=140 (PDIHS) 138 146 144 145 28 type=141 (PDIHS) 144 148 146 147 Ryckaert-Bell.: nr: 1565 iatoms: 0 type=143 (RBDIHS) 1 0 4 5 1 type=144 (RBDIHS) 1 0 4 6 2 type=144 (RBDIHS) 1 0 4 22 3 type=143 (RBDIHS) 2 0 4 5 4 type=144 (RBDIHS) 2 0 4 6 5 type=144 (RBDIHS) 2 0 4 22 6 type=143 (RBDIHS) 3 0 4 5 7 type=144 (RBDIHS) 3 0 4 6 8 type=144 (RBDIHS) 3 0 4 22 9 type=145 (RBDIHS) 0 4 6 9 10 type=146 (RBDIHS) 22 4 6 9 11 type=147 (RBDIHS) 0 4 6 7 12 type=147 (RBDIHS) 0 4 6 8 13 type=148 (RBDIHS) 5 4 6 7 14 type=148 (RBDIHS) 5 4 6 8 15 type=148 (RBDIHS) 5 4 6 9 16 type=149 (RBDIHS) 22 4 6 7 17 type=149 (RBDIHS) 22 4 6 8 18 type=150 (RBDIHS) 0 4 22 24 19 type=151 (RBDIHS) 6 4 22 24 20 type=148 (RBDIHS) 4 6 9 10 21 type=148 (RBDIHS) 4 6 9 11 22 type=152 (RBDIHS) 4 6 9 12 23 type=148 (RBDIHS) 7 6 9 10 24 type=148 (RBDIHS) 7 6 9 11 25 type=148 (RBDIHS) 7 6 9 12 26 type=148 (RBDIHS) 8 6 9 10 27 type=148 (RBDIHS) 8 6 9 11 28 type=148 (RBDIHS) 8 6 9 12 29 type=148 (RBDIHS) 6 9 12 13 30 type=148 (RBDIHS) 6 9 12 14 31 type=152 (RBDIHS) 6 9 12 15 32 type=148 (RBDIHS) 10 9 12 13 33 type=148 (RBDIHS) 10 9 12 14 34 type=148 (RBDIHS) 10 9 12 15 35 type=148 (RBDIHS) 11 9 12 13 36 type=148 (RBDIHS) 11 9 12 14 37 type=148 (RBDIHS) 11 9 12 15 38 type=148 (RBDIHS) 9 12 15 16 39 type=148 (RBDIHS) 9 12 15 17 40 type=153 (RBDIHS) 9 12 15 18 41 type=148 (RBDIHS) 13 12 15 16 42 type=148 (RBDIHS) 13 12 15 17 43 type=154 (RBDIHS) 13 12 15 18 44 type=148 (RBDIHS) 14 12 15 16 45 type=148 (RBDIHS) 14 12 15 17 46 type=154 (RBDIHS) 14 12 15 18 47 type=144 (RBDIHS) 12 15 18 19 48 type=144 (RBDIHS) 12 15 18 20 49 type=144 (RBDIHS) 12 15 18 21 50 type=143 (RBDIHS) 16 15 18 19 51 type=143 (RBDIHS) 16 15 18 20 52 type=143 (RBDIHS) 16 15 18 21 53 type=143 (RBDIHS) 17 15 18 19 54 type=143 (RBDIHS) 17 15 18 20 55 type=143 (RBDIHS) 17 15 18 21 56 type=155 (RBDIHS) 4 22 24 25 57 type=156 (RBDIHS) 4 22 24 26 58 type=155 (RBDIHS) 23 22 24 25 59 type=157 (RBDIHS) 23 22 24 26 60 type=158 (RBDIHS) 22 24 26 28 61 type=159 (RBDIHS) 22 24 26 38 62 type=160 (RBDIHS) 24 26 28 30 63 type=160 (RBDIHS) 24 26 28 34 64 type=161 (RBDIHS) 38 26 28 30 65 type=161 (RBDIHS) 38 26 28 34 66 type=147 (RBDIHS) 24 26 28 29 67 type=148 (RBDIHS) 27 26 28 29 68 type=148 (RBDIHS) 27 26 28 30 69 type=148 (RBDIHS) 27 26 28 34 70 type=149 (RBDIHS) 38 26 28 29 71 type=150 (RBDIHS) 24 26 38 40 72 type=151 (RBDIHS) 28 26 38 40 73 type=148 (RBDIHS) 26 28 30 31 74 type=148 (RBDIHS) 26 28 30 32 75 type=148 (RBDIHS) 26 28 30 33 76 type=148 (RBDIHS) 29 28 30 31 77 type=148 (RBDIHS) 29 28 30 32 78 type=148 (RBDIHS) 29 28 30 33 79 type=148 (RBDIHS) 34 28 30 31 80 type=148 (RBDIHS) 34 28 30 32 81 type=148 (RBDIHS) 34 28 30 33 82 type=148 (RBDIHS) 26 28 34 35 83 type=148 (RBDIHS) 26 28 34 36 84 type=148 (RBDIHS) 26 28 34 37 85 type=148 (RBDIHS) 29 28 34 35 86 type=148 (RBDIHS) 29 28 34 36 87 type=148 (RBDIHS) 29 28 34 37 88 type=148 (RBDIHS) 30 28 34 35 89 type=148 (RBDIHS) 30 28 34 36 90 type=148 (RBDIHS) 30 28 34 37 91 type=155 (RBDIHS) 26 38 40 41 92 type=156 (RBDIHS) 26 38 40 42 93 type=155 (RBDIHS) 39 38 40 41 94 type=157 (RBDIHS) 39 38 40 42 95 type=158 (RBDIHS) 38 40 42 44 96 type=159 (RBDIHS) 38 40 42 58 97 type=147 (RBDIHS) 40 42 44 45 98 type=147 (RBDIHS) 40 42 44 46 99 type=162 (RBDIHS) 40 42 44 47 100 type=148 (RBDIHS) 43 42 44 45 101 type=148 (RBDIHS) 43 42 44 46 102 type=163 (RBDIHS) 43 42 44 47 103 type=149 (RBDIHS) 58 42 44 45 104 type=149 (RBDIHS) 58 42 44 46 105 type=164 (RBDIHS) 58 42 44 47 106 type=150 (RBDIHS) 40 42 58 60 107 type=151 (RBDIHS) 44 42 58 60 108 type=165 (RBDIHS) 44 47 48 49 109 type=165 (RBDIHS) 44 47 48 52 110 type=165 (RBDIHS) 50 47 48 49 111 type=165 (RBDIHS) 50 47 48 52 112 type=165 (RBDIHS) 44 47 50 51 113 type=165 (RBDIHS) 44 47 50 54 114 type=165 (RBDIHS) 48 47 50 51 115 type=165 (RBDIHS) 48 47 50 54 116 type=165 (RBDIHS) 47 48 52 53 117 type=165 (RBDIHS) 47 48 52 56 118 type=165 (RBDIHS) 49 48 52 53 119 type=165 (RBDIHS) 49 48 52 56 120 type=165 (RBDIHS) 47 50 54 55 121 type=165 (RBDIHS) 47 50 54 56 122 type=165 (RBDIHS) 51 50 54 55 123 type=165 (RBDIHS) 51 50 54 56 124 type=165 (RBDIHS) 48 52 56 54 125 type=165 (RBDIHS) 48 52 56 57 126 type=165 (RBDIHS) 53 52 56 54 127 type=165 (RBDIHS) 53 52 56 57 128 type=165 (RBDIHS) 50 54 56 52 129 type=165 (RBDIHS) 50 54 56 57 130 type=165 (RBDIHS) 55 54 56 52 131 type=165 (RBDIHS) 55 54 56 57 132 type=155 (RBDIHS) 42 58 60 61 133 type=156 (RBDIHS) 42 58 60 62 134 type=155 (RBDIHS) 59 58 60 61 135 type=157 (RBDIHS) 59 58 60 62 136 type=159 (RBDIHS) 58 60 62 65 137 type=150 (RBDIHS) 60 62 65 67 138 type=155 (RBDIHS) 62 65 67 68 139 type=156 (RBDIHS) 62 65 67 69 140 type=155 (RBDIHS) 66 65 67 68 141 type=157 (RBDIHS) 66 65 67 69 142 type=158 (RBDIHS) 65 67 69 71 143 type=159 (RBDIHS) 65 67 69 89 144 type=166 (RBDIHS) 67 69 71 74 145 type=167 (RBDIHS) 89 69 71 74 146 type=147 (RBDIHS) 67 69 71 72 147 type=147 (RBDIHS) 67 69 71 73 148 type=148 (RBDIHS) 70 69 71 72 149 type=148 (RBDIHS) 70 69 71 73 150 type=148 (RBDIHS) 70 69 71 74 151 type=149 (RBDIHS) 89 69 71 72 152 type=149 (RBDIHS) 89 69 71 73 153 type=150 (RBDIHS) 67 69 89 91 154 type=151 (RBDIHS) 71 69 89 91 155 type=148 (RBDIHS) 69 71 74 75 156 type=148 (RBDIHS) 69 71 74 76 157 type=152 (RBDIHS) 69 71 74 77 158 type=148 (RBDIHS) 72 71 74 75 159 type=148 (RBDIHS) 72 71 74 76 160 type=148 (RBDIHS) 72 71 74 77 161 type=148 (RBDIHS) 73 71 74 75 162 type=148 (RBDIHS) 73 71 74 76 163 type=148 (RBDIHS) 73 71 74 77 164 type=148 (RBDIHS) 71 74 77 78 165 type=148 (RBDIHS) 71 74 77 79 166 type=153 (RBDIHS) 71 74 77 80 167 type=148 (RBDIHS) 75 74 77 78 168 type=148 (RBDIHS) 75 74 77 79 169 type=168 (RBDIHS) 75 74 77 80 170 type=148 (RBDIHS) 76 74 77 78 171 type=148 (RBDIHS) 76 74 77 79 172 type=168 (RBDIHS) 76 74 77 80 173 type=169 (RBDIHS) 74 77 80 81 174 type=170 (RBDIHS) 74 77 80 82 175 type=171 (RBDIHS) 78 77 80 82 176 type=171 (RBDIHS) 79 77 80 82 177 type=172 (RBDIHS) 77 80 82 83 178 type=172 (RBDIHS) 77 80 82 86 179 type=173 (RBDIHS) 81 80 82 83 180 type=173 (RBDIHS) 81 80 82 86 181 type=173 (RBDIHS) 80 82 83 84 182 type=173 (RBDIHS) 80 82 83 85 183 type=173 (RBDIHS) 86 82 83 84 184 type=173 (RBDIHS) 86 82 83 85 185 type=173 (RBDIHS) 80 82 86 87 186 type=173 (RBDIHS) 80 82 86 88 187 type=173 (RBDIHS) 83 82 86 87 188 type=173 (RBDIHS) 83 82 86 88 189 type=155 (RBDIHS) 69 89 91 92 190 type=156 (RBDIHS) 69 89 91 93 191 type=155 (RBDIHS) 90 89 91 92 192 type=157 (RBDIHS) 90 89 91 93 193 type=158 (RBDIHS) 89 91 93 95 194 type=159 (RBDIHS) 89 91 93 100 195 type=174 (RBDIHS) 91 93 95 98 196 type=175 (RBDIHS) 100 93 95 98 197 type=147 (RBDIHS) 91 93 95 96 198 type=147 (RBDIHS) 91 93 95 97 199 type=148 (RBDIHS) 94 93 95 96 200 type=148 (RBDIHS) 94 93 95 97 201 type=176 (RBDIHS) 94 93 95 98 202 type=149 (RBDIHS) 100 93 95 96 203 type=149 (RBDIHS) 100 93 95 97 204 type=150 (RBDIHS) 91 93 100 102 205 type=151 (RBDIHS) 95 93 100 102 206 type=177 (RBDIHS) 93 95 98 99 207 type=178 (RBDIHS) 96 95 98 99 208 type=178 (RBDIHS) 97 95 98 99 209 type=155 (RBDIHS) 93 100 102 103 210 type=156 (RBDIHS) 93 100 102 104 211 type=155 (RBDIHS) 101 100 102 103 212 type=157 (RBDIHS) 101 100 102 104 213 type=158 (RBDIHS) 100 102 104 106 214 type=159 (RBDIHS) 100 102 104 115 215 type=179 (RBDIHS) 102 104 106 109 216 type=180 (RBDIHS) 115 104 106 109 217 type=147 (RBDIHS) 102 104 106 107 218 type=147 (RBDIHS) 102 104 106 108 219 type=148 (RBDIHS) 105 104 106 107 220 type=148 (RBDIHS) 105 104 106 108 221 type=148 (RBDIHS) 105 104 106 109 222 type=149 (RBDIHS) 115 104 106 107 223 type=149 (RBDIHS) 115 104 106 108 224 type=150 (RBDIHS) 102 104 115 117 225 type=151 (RBDIHS) 106 104 115 117 226 type=148 (RBDIHS) 104 106 109 110 227 type=148 (RBDIHS) 104 106 109 111 228 type=181 (RBDIHS) 104 106 109 112 229 type=148 (RBDIHS) 107 106 109 110 230 type=148 (RBDIHS) 107 106 109 111 231 type=182 (RBDIHS) 107 106 109 112 232 type=148 (RBDIHS) 108 106 109 110 233 type=148 (RBDIHS) 108 106 109 111 234 type=182 (RBDIHS) 108 106 109 112 235 type=183 (RBDIHS) 106 109 112 113 236 type=183 (RBDIHS) 106 109 112 114 237 type=155 (RBDIHS) 104 115 117 118 238 type=156 (RBDIHS) 104 115 117 119 239 type=155 (RBDIHS) 116 115 117 118 240 type=157 (RBDIHS) 116 115 117 119 241 type=158 (RBDIHS) 115 117 119 121 242 type=159 (RBDIHS) 115 117 119 134 243 type=184 (RBDIHS) 117 119 121 124 244 type=185 (RBDIHS) 134 119 121 124 245 type=147 (RBDIHS) 117 119 121 122 246 type=147 (RBDIHS) 117 119 121 123 247 type=148 (RBDIHS) 120 119 121 122 248 type=148 (RBDIHS) 120 119 121 123 249 type=148 (RBDIHS) 120 119 121 124 250 type=149 (RBDIHS) 134 119 121 122 251 type=149 (RBDIHS) 134 119 121 123 252 type=150 (RBDIHS) 117 119 134 136 253 type=151 (RBDIHS) 121 119 134 136 254 type=148 (RBDIHS) 119 121 124 125 255 type=152 (RBDIHS) 119 121 124 126 256 type=152 (RBDIHS) 119 121 124 130 257 type=148 (RBDIHS) 122 121 124 125 258 type=148 (RBDIHS) 122 121 124 126 259 type=148 (RBDIHS) 122 121 124 130 260 type=148 (RBDIHS) 123 121 124 125 261 type=148 (RBDIHS) 123 121 124 126 262 type=148 (RBDIHS) 123 121 124 130 263 type=148 (RBDIHS) 121 124 126 127 264 type=148 (RBDIHS) 121 124 126 128 265 type=148 (RBDIHS) 121 124 126 129 266 type=148 (RBDIHS) 125 124 126 127 267 type=148 (RBDIHS) 125 124 126 128 268 type=148 (RBDIHS) 125 124 126 129 269 type=148 (RBDIHS) 130 124 126 127 270 type=148 (RBDIHS) 130 124 126 128 271 type=148 (RBDIHS) 130 124 126 129 272 type=148 (RBDIHS) 121 124 130 131 273 type=148 (RBDIHS) 121 124 130 132 274 type=148 (RBDIHS) 121 124 130 133 275 type=148 (RBDIHS) 125 124 130 131 276 type=148 (RBDIHS) 125 124 130 132 277 type=148 (RBDIHS) 125 124 130 133 278 type=148 (RBDIHS) 126 124 130 131 279 type=148 (RBDIHS) 126 124 130 132 280 type=148 (RBDIHS) 126 124 130 133 281 type=155 (RBDIHS) 119 134 136 137 282 type=156 (RBDIHS) 119 134 136 138 283 type=155 (RBDIHS) 135 134 136 137 284 type=157 (RBDIHS) 135 134 136 138 285 type=158 (RBDIHS) 134 136 138 140 286 type=159 (RBDIHS) 134 136 138 144 287 type=147 (RBDIHS) 136 138 140 141 288 type=147 (RBDIHS) 136 138 140 142 289 type=147 (RBDIHS) 136 138 140 143 290 type=148 (RBDIHS) 139 138 140 141 291 type=148 (RBDIHS) 139 138 140 142 292 type=148 (RBDIHS) 139 138 140 143 293 type=149 (RBDIHS) 144 138 140 141 294 type=149 (RBDIHS) 144 138 140 142 295 type=149 (RBDIHS) 144 138 140 143 296 type=150 (RBDIHS) 136 138 144 146 297 type=151 (RBDIHS) 140 138 144 146 298 type=155 (RBDIHS) 138 144 146 147 299 type=156 (RBDIHS) 138 144 146 148 300 type=155 (RBDIHS) 145 144 146 147 301 type=157 (RBDIHS) 145 144 146 148 302 type=158 (RBDIHS) 144 146 148 150 303 type=159 (RBDIHS) 144 146 148 154 304 type=147 (RBDIHS) 146 148 150 151 305 type=147 (RBDIHS) 146 148 150 152 306 type=147 (RBDIHS) 146 148 150 153 307 type=148 (RBDIHS) 149 148 150 151 308 type=148 (RBDIHS) 149 148 150 152 309 type=148 (RBDIHS) 149 148 150 153 310 type=149 (RBDIHS) 154 148 150 151 311 type=149 (RBDIHS) 154 148 150 152 312 type=149 (RBDIHS) 154 148 150 153 Restricted Dih.: nr: 0 CBT Dih.: nr: 0 Fourier Dih.: nr: 0 Improper Dih.: nr: 0 Periodic Improper Dih.: nr: 0 Tab. Dih.: nr: 0 CMAP Dih.: nr: 0 GB 1-2 Pol. (unused): nr: 0 GB 1-3 Pol. (unused): nr: 0 GB 1-4 Pol. (unused): nr: 0 GB Polarization (unused): nr: 0 Nonpolar Sol. (unused): nr: 0 LJ-14: nr: 1197 iatoms: 0 type=186 (LJ14) 0 7 1 type=186 (LJ14) 0 8 2 type=187 (LJ14) 0 9 3 type=188 (LJ14) 0 23 4 type=189 (LJ14) 0 24 5 type=190 (LJ14) 1 5 6 type=190 (LJ14) 1 6 7 type=190 (LJ14) 1 22 8 type=190 (LJ14) 2 5 9 type=190 (LJ14) 2 6 10 type=190 (LJ14) 2 22 11 type=190 (LJ14) 3 5 12 type=190 (LJ14) 3 6 13 type=190 (LJ14) 3 22 14 type=191 (LJ14) 4 10 15 type=191 (LJ14) 4 11 16 type=192 (LJ14) 4 12 17 type=190 (LJ14) 4 25 18 type=192 (LJ14) 4 26 19 type=193 (LJ14) 5 7 20 type=193 (LJ14) 5 8 21 type=191 (LJ14) 5 9 22 type=194 (LJ14) 5 23 23 type=186 (LJ14) 5 24 24 type=191 (LJ14) 6 13 25 type=191 (LJ14) 6 14 26 type=192 (LJ14) 6 15 27 type=195 (LJ14) 6 23 28 type=187 (LJ14) 6 24 29 type=193 (LJ14) 7 10 30 type=193 (LJ14) 7 11 31 type=191 (LJ14) 7 12 32 type=196 (LJ14) 7 22 33 type=193 (LJ14) 8 10 34 type=193 (LJ14) 8 11 35 type=191 (LJ14) 8 12 36 type=196 (LJ14) 8 22 37 type=191 (LJ14) 9 16 38 type=191 (LJ14) 9 17 39 type=187 (LJ14) 9 18 40 type=197 (LJ14) 9 22 41 type=193 (LJ14) 10 13 42 type=193 (LJ14) 10 14 43 type=191 (LJ14) 10 15 44 type=193 (LJ14) 11 13 45 type=193 (LJ14) 11 14 46 type=191 (LJ14) 11 15 47 type=190 (LJ14) 12 19 48 type=190 (LJ14) 12 20 49 type=190 (LJ14) 12 21 50 type=193 (LJ14) 13 16 51 type=193 (LJ14) 13 17 52 type=186 (LJ14) 13 18 53 type=193 (LJ14) 14 16 54 type=193 (LJ14) 14 17 55 type=186 (LJ14) 14 18 56 type=190 (LJ14) 16 19 57 type=190 (LJ14) 16 20 58 type=190 (LJ14) 16 21 59 type=190 (LJ14) 17 19 60 type=190 (LJ14) 17 20 61 type=190 (LJ14) 17 21 62 type=196 (LJ14) 22 27 63 type=197 (LJ14) 22 28 64 type=198 (LJ14) 22 38 65 type=190 (LJ14) 23 25 66 type=195 (LJ14) 23 26 67 type=186 (LJ14) 24 29 68 type=187 (LJ14) 24 30 69 type=187 (LJ14) 24 34 70 type=188 (LJ14) 24 39 71 type=189 (LJ14) 24 40 72 type=190 (LJ14) 25 27 73 type=190 (LJ14) 25 28 74 type=190 (LJ14) 25 38 75 type=191 (LJ14) 26 31 76 type=191 (LJ14) 26 32 77 type=191 (LJ14) 26 33 78 type=191 (LJ14) 26 35 79 type=191 (LJ14) 26 36 80 type=191 (LJ14) 26 37 81 type=190 (LJ14) 26 41 82 type=192 (LJ14) 26 42 83 type=193 (LJ14) 27 29 84 type=191 (LJ14) 27 30 85 type=191 (LJ14) 27 34 86 type=194 (LJ14) 27 39 87 type=186 (LJ14) 27 40 88 type=195 (LJ14) 28 39 89 type=187 (LJ14) 28 40 90 type=193 (LJ14) 29 31 91 type=193 (LJ14) 29 32 92 type=193 (LJ14) 29 33 93 type=193 (LJ14) 29 35 94 type=193 (LJ14) 29 36 95 type=193 (LJ14) 29 37 96 type=196 (LJ14) 29 38 97 type=191 (LJ14) 30 35 98 type=191 (LJ14) 30 36 99 type=191 (LJ14) 30 37 100 type=197 (LJ14) 30 38 101 type=191 (LJ14) 31 34 102 type=191 (LJ14) 32 34 103 type=191 (LJ14) 33 34 104 type=197 (LJ14) 34 38 105 type=196 (LJ14) 38 43 106 type=197 (LJ14) 38 44 107 type=198 (LJ14) 38 58 108 type=190 (LJ14) 39 41 109 type=195 (LJ14) 39 42 110 type=186 (LJ14) 40 45 111 type=186 (LJ14) 40 46 112 type=199 (LJ14) 40 47 113 type=188 (LJ14) 40 59 114 type=189 (LJ14) 40 60 115 type=190 (LJ14) 41 43 116 type=190 (LJ14) 41 44 117 type=190 (LJ14) 41 58 118 type=200 (LJ14) 42 48 119 type=200 (LJ14) 42 50 120 type=190 (LJ14) 42 61 121 type=192 (LJ14) 42 62 122 type=193 (LJ14) 43 45 123 type=193 (LJ14) 43 46 124 type=201 (LJ14) 43 47 125 type=194 (LJ14) 43 59 126 type=186 (LJ14) 43 60 127 type=202 (LJ14) 44 49 128 type=202 (LJ14) 44 51 129 type=200 (LJ14) 44 52 130 type=200 (LJ14) 44 54 131 type=195 (LJ14) 44 59 132 type=187 (LJ14) 44 60 133 type=201 (LJ14) 45 48 134 type=201 (LJ14) 45 50 135 type=196 (LJ14) 45 58 136 type=201 (LJ14) 46 48 137 type=201 (LJ14) 46 50 138 type=196 (LJ14) 46 58 139 type=203 (LJ14) 47 53 140 type=203 (LJ14) 47 55 141 type=204 (LJ14) 47 56 142 type=205 (LJ14) 47 58 143 type=203 (LJ14) 48 51 144 type=204 (LJ14) 48 54 145 type=203 (LJ14) 48 57 146 type=203 (LJ14) 49 50 147 type=206 (LJ14) 49 53 148 type=203 (LJ14) 49 56 149 type=204 (LJ14) 50 52 150 type=203 (LJ14) 50 57 151 type=206 (LJ14) 51 55 152 type=203 (LJ14) 51 56 153 type=203 (LJ14) 52 55 154 type=203 (LJ14) 53 54 155 type=206 (LJ14) 53 57 156 type=206 (LJ14) 55 57 157 type=196 (LJ14) 58 63 158 type=196 (LJ14) 58 64 159 type=198 (LJ14) 58 65 160 type=190 (LJ14) 59 61 161 type=195 (LJ14) 59 62 162 type=188 (LJ14) 60 66 163 type=189 (LJ14) 60 67 164 type=190 (LJ14) 61 63 165 type=190 (LJ14) 61 64 166 type=190 (LJ14) 61 65 167 type=190 (LJ14) 62 68 168 type=192 (LJ14) 62 69 169 type=194 (LJ14) 63 66 170 type=186 (LJ14) 63 67 171 type=194 (LJ14) 64 66 172 type=186 (LJ14) 64 67 173 type=196 (LJ14) 65 70 174 type=197 (LJ14) 65 71 175 type=198 (LJ14) 65 89 176 type=190 (LJ14) 66 68 177 type=195 (LJ14) 66 69 178 type=186 (LJ14) 67 72 179 type=186 (LJ14) 67 73 180 type=187 (LJ14) 67 74 181 type=188 (LJ14) 67 90 182 type=189 (LJ14) 67 91 183 type=190 (LJ14) 68 70 184 type=190 (LJ14) 68 71 185 type=190 (LJ14) 68 89 186 type=191 (LJ14) 69 75 187 type=191 (LJ14) 69 76 188 type=192 (LJ14) 69 77 189 type=190 (LJ14) 69 92 190 type=192 (LJ14) 69 93 191 type=193 (LJ14) 70 72 192 type=193 (LJ14) 70 73 193 type=191 (LJ14) 70 74 194 type=194 (LJ14) 70 90 195 type=186 (LJ14) 70 91 196 type=191 (LJ14) 71 78 197 type=191 (LJ14) 71 79 198 type=187 (LJ14) 71 80 199 type=195 (LJ14) 71 90 200 type=187 (LJ14) 71 91 201 type=193 (LJ14) 72 75 202 type=193 (LJ14) 72 76 203 type=191 (LJ14) 72 77 204 type=196 (LJ14) 72 89 205 type=193 (LJ14) 73 75 206 type=193 (LJ14) 73 76 207 type=191 (LJ14) 73 77 208 type=196 (LJ14) 73 89 209 type=190 (LJ14) 74 81 210 type=207 (LJ14) 74 82 211 type=197 (LJ14) 74 89 212 type=193 (LJ14) 75 78 213 type=193 (LJ14) 75 79 214 type=186 (LJ14) 75 80 215 type=193 (LJ14) 76 78 216 type=193 (LJ14) 76 79 217 type=186 (LJ14) 76 80 218 type=187 (LJ14) 77 83 219 type=187 (LJ14) 77 86 220 type=190 (LJ14) 78 81 221 type=208 (LJ14) 78 82 222 type=190 (LJ14) 79 81 223 type=208 (LJ14) 79 82 224 type=190 (LJ14) 80 84 225 type=190 (LJ14) 80 85 226 type=190 (LJ14) 80 87 227 type=190 (LJ14) 80 88 228 type=190 (LJ14) 81 83 229 type=190 (LJ14) 81 86 230 type=190 (LJ14) 83 87 231 type=190 (LJ14) 83 88 232 type=190 (LJ14) 84 86 233 type=190 (LJ14) 85 86 234 type=196 (LJ14) 89 94 235 type=197 (LJ14) 89 95 236 type=198 (LJ14) 89 100 237 type=190 (LJ14) 90 92 238 type=195 (LJ14) 90 93 239 type=186 (LJ14) 91 96 240 type=186 (LJ14) 91 97 241 type=209 (LJ14) 91 98 242 type=188 (LJ14) 91 101 243 type=189 (LJ14) 91 102 244 type=190 (LJ14) 92 94 245 type=190 (LJ14) 92 95 246 type=190 (LJ14) 92 100 247 type=190 (LJ14) 93 99 248 type=190 (LJ14) 93 103 249 type=192 (LJ14) 93 104 250 type=193 (LJ14) 94 96 251 type=193 (LJ14) 94 97 252 type=210 (LJ14) 94 98 253 type=194 (LJ14) 94 101 254 type=186 (LJ14) 94 102 255 type=195 (LJ14) 95 101 256 type=187 (LJ14) 95 102 257 type=190 (LJ14) 96 99 258 type=196 (LJ14) 96 100 259 type=190 (LJ14) 97 99 260 type=196 (LJ14) 97 100 261 type=211 (LJ14) 98 100 262 type=196 (LJ14) 100 105 263 type=197 (LJ14) 100 106 264 type=198 (LJ14) 100 115 265 type=190 (LJ14) 101 103 266 type=195 (LJ14) 101 104 267 type=186 (LJ14) 102 107 268 type=186 (LJ14) 102 108 269 type=187 (LJ14) 102 109 270 type=188 (LJ14) 102 116 271 type=189 (LJ14) 102 117 272 type=190 (LJ14) 103 105 273 type=190 (LJ14) 103 106 274 type=190 (LJ14) 103 115 275 type=191 (LJ14) 104 110 276 type=191 (LJ14) 104 111 277 type=197 (LJ14) 104 112 278 type=190 (LJ14) 104 118 279 type=192 (LJ14) 104 119 280 type=193 (LJ14) 105 107 281 type=193 (LJ14) 105 108 282 type=191 (LJ14) 105 109 283 type=194 (LJ14) 105 116 284 type=186 (LJ14) 105 117 285 type=195 (LJ14) 106 113 286 type=195 (LJ14) 106 114 287 type=195 (LJ14) 106 116 288 type=187 (LJ14) 106 117 289 type=193 (LJ14) 107 110 290 type=193 (LJ14) 107 111 291 type=196 (LJ14) 107 112 292 type=196 (LJ14) 107 115 293 type=193 (LJ14) 108 110 294 type=193 (LJ14) 108 111 295 type=196 (LJ14) 108 112 296 type=196 (LJ14) 108 115 297 type=197 (LJ14) 109 115 298 type=194 (LJ14) 110 113 299 type=194 (LJ14) 110 114 300 type=194 (LJ14) 111 113 301 type=194 (LJ14) 111 114 302 type=196 (LJ14) 115 120 303 type=197 (LJ14) 115 121 304 type=198 (LJ14) 115 134 305 type=190 (LJ14) 116 118 306 type=195 (LJ14) 116 119 307 type=186 (LJ14) 117 122 308 type=186 (LJ14) 117 123 309 type=187 (LJ14) 117 124 310 type=188 (LJ14) 117 135 311 type=189 (LJ14) 117 136 312 type=190 (LJ14) 118 120 313 type=190 (LJ14) 118 121 314 type=190 (LJ14) 118 134 315 type=191 (LJ14) 119 125 316 type=192 (LJ14) 119 126 317 type=192 (LJ14) 119 130 318 type=190 (LJ14) 119 137 319 type=192 (LJ14) 119 138 320 type=193 (LJ14) 120 122 321 type=193 (LJ14) 120 123 322 type=191 (LJ14) 120 124 323 type=194 (LJ14) 120 135 324 type=186 (LJ14) 120 136 325 type=191 (LJ14) 121 127 326 type=191 (LJ14) 121 128 327 type=191 (LJ14) 121 129 328 type=191 (LJ14) 121 131 329 type=191 (LJ14) 121 132 330 type=191 (LJ14) 121 133 331 type=195 (LJ14) 121 135 332 type=187 (LJ14) 121 136 333 type=193 (LJ14) 122 125 334 type=191 (LJ14) 122 126 335 type=191 (LJ14) 122 130 336 type=196 (LJ14) 122 134 337 type=193 (LJ14) 123 125 338 type=191 (LJ14) 123 126 339 type=191 (LJ14) 123 130 340 type=196 (LJ14) 123 134 341 type=197 (LJ14) 124 134 342 type=193 (LJ14) 125 127 343 type=193 (LJ14) 125 128 344 type=193 (LJ14) 125 129 345 type=193 (LJ14) 125 131 346 type=193 (LJ14) 125 132 347 type=193 (LJ14) 125 133 348 type=191 (LJ14) 126 131 349 type=191 (LJ14) 126 132 350 type=191 (LJ14) 126 133 351 type=191 (LJ14) 127 130 352 type=191 (LJ14) 128 130 353 type=191 (LJ14) 129 130 354 type=196 (LJ14) 134 139 355 type=197 (LJ14) 134 140 356 type=198 (LJ14) 134 144 357 type=190 (LJ14) 135 137 358 type=195 (LJ14) 135 138 359 type=186 (LJ14) 136 141 360 type=186 (LJ14) 136 142 361 type=186 (LJ14) 136 143 362 type=188 (LJ14) 136 145 363 type=189 (LJ14) 136 146 364 type=190 (LJ14) 137 139 365 type=190 (LJ14) 137 140 366 type=190 (LJ14) 137 144 367 type=190 (LJ14) 138 147 368 type=192 (LJ14) 138 148 369 type=193 (LJ14) 139 141 370 type=193 (LJ14) 139 142 371 type=193 (LJ14) 139 143 372 type=194 (LJ14) 139 145 373 type=186 (LJ14) 139 146 374 type=195 (LJ14) 140 145 375 type=187 (LJ14) 140 146 376 type=196 (LJ14) 141 144 377 type=196 (LJ14) 142 144 378 type=196 (LJ14) 143 144 379 type=196 (LJ14) 144 149 380 type=197 (LJ14) 144 150 381 type=198 (LJ14) 144 154 382 type=190 (LJ14) 145 147 383 type=195 (LJ14) 145 148 384 type=186 (LJ14) 146 151 385 type=186 (LJ14) 146 152 386 type=186 (LJ14) 146 153 387 type=188 (LJ14) 146 155 388 type=190 (LJ14) 147 149 389 type=190 (LJ14) 147 150 390 type=190 (LJ14) 147 154 391 type=193 (LJ14) 149 151 392 type=193 (LJ14) 149 152 393 type=193 (LJ14) 149 153 394 type=194 (LJ14) 149 155 395 type=195 (LJ14) 150 155 396 type=196 (LJ14) 151 154 397 type=196 (LJ14) 152 154 398 type=196 (LJ14) 153 154 Coulomb-14: nr: 0 LJC-14 q: nr: 0 LJC Pairs NB: nr: 0 LJ (SR): nr: 0 Buck.ham (SR): nr: 0 LJ (unused): nr: 0 B.ham (unused): nr: 0 Disper. corr.: nr: 0 Coulomb (SR): nr: 0 Coul (unused): nr: 0 RF excl.: nr: 0 Coul. recip.: nr: 0 LJ recip.: nr: 0 DPD: nr: 0 Polarization: nr: 0 Water Pol.: nr: 0 Thole Pol.: nr: 0 Anharm. Pol.: nr: 0 Position Rest.: nr: 0 Flat-bottom posres: nr: 0 Dis. Rest.: nr: 0 D.R.Viol. (nm): nr: 0 Orient. Rest.: nr: 0 Ori. R. RMSD: nr: 0 Angle Rest.: nr: 0 Angle Rest. Z: nr: 0 Dih. Rest.: nr: 0 Dih. Rest. Viol.: nr: 0 Constraint: nr: 0 Constr. No Conn.: nr: 0 Settle: nr: 0 Virtual site 1: nr: 0 Virtual site 2: nr: 0 Virtual site 2fd: nr: 0 Virtual site 3: nr: 0 Virtual site 3fd: nr: 0 Virtual site 3fad: nr: 0 Virtual site 3out: nr: 0 Virtual site 4fd: nr: 0 Virtual site 4fdn: nr: 0 Virtual site N: nr: 0 COM Pull En.: nr: 0 Density fitting: nr: 0 Quantum En.: nr: 0 Potential: nr: 0 Kinetic En.: nr: 0 Total Energy: nr: 0 Conserved En.: nr: 0 Temperature: nr: 0 Vir. Temp. (not used): nr: 0 Pres. DC: nr: 0 Pressure: nr: 0 dH/dl constr.: nr: 0 dVremain/dl: nr: 0 dEkin/dl: nr: 0 dVcoul/dl: nr: 0 dVvdw/dl: nr: 0 dVbonded/dl: nr: 0 dVrestraint/dl: nr: 0 dVtemperature/dl: nr: 0 grp[T-Coupling ] nr=1, name=[ rest] grp[Energy Mon. ] nr=1, name=[ rest] grp[Acc. not used] nr=1, name=[ rest] grp[Freeze ] nr=1, name=[ rest] grp[User1 ] nr=1, name=[ rest] grp[User2 ] nr=1, name=[ rest] grp[VCM ] nr=1, name=[ rest] grp[Compressed X] nr=1, name=[ rest] grp[Or. Res. Fit] nr=1, name=[ rest] grp[QMMM ] nr=1, name=[ rest] grpname (11): grpname[0]={name="System"} grpname[1]={name="Protein"} grpname[2]={name="Protein-H"} grpname[3]={name="C-alpha"} grpname[4]={name="Backbone"} grpname[5]={name="MainChain"} grpname[6]={name="MainChain+Cb"} grpname[7]={name="MainChain+H"} grpname[8]={name="SideChain"} grpname[9]={name="SideChain-H"} grpname[10]={name="rest"} groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM allocated 0 0 0 0 0 0 0 0 0 0 groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 box (3x3): box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} box_rel (3x3): box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} boxv (3x3): boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev (3x3): pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev (3x3): svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev (3x3): fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} nosehoover_xi: not available x (156x3): x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} v (156x3): v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} Group statistics T-Coupling : 156 (total 156 atoms) Energy Mon. : 156 (total 156 atoms) Acc. not used: 156 (total 156 atoms) Freeze : 156 (total 156 atoms) User1 : 156 (total 156 atoms) User2 : 156 (total 156 atoms) VCM : 156 (total 156 atoms) Compressed X: 156 (total 156 atoms) Or. Res. Fit: 156 (total 156 atoms) QMMM : 156 (total 156 atoms) [ OK ] DumpTest.WorksWithTpr (5 ms) [ RUN ] DumpTest.WorksWithTprAndMdpWriting Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022 (single precision) [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms) [----------] 2 tests from DumpTest (7 ms total) [----------] 3 tests from HelpwritingTest [ RUN ] HelpwritingTest.ConvertTprWritesHelp [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms) [ RUN ] HelpwritingTest.DumpWritesHelp [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) [ RUN ] HelpwritingTest.ReportMethodsWritesHelp [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) [----------] 3 tests from HelpwritingTest (2 ms total) [----------] 4 tests from ReportMethodsTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Setting the LD random seed to -203423771 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) [ RUN ] ReportMethodsTest.WritesCorrectInformation Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022 (single precision) [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) [ RUN ] ReportMethodsTest.ToolEndToEndTest Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022 (single precision) section: Methods subsection: Simulation system A system of 1 molecules (156 atoms) was simulated. subsection: Simulation settings A total of 0 ns were simulated with a time step of 1 fs. Neighbor searching was performed every 10 steps. The Cut-off algorithm was used for electrostatic interactions. with a cut-off of 1 nm. A single cut-off of 1.1 nm was used for Van der Waals interactions. [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) [----------] 4 tests from ReportMethodsTest (2 ms total) [----------] 3 tests from ConvertTprTest [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2022 (single precision) Setting the LD random seed to 1610575855 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data Input file: Run start step 0 Run start time 0 ps Step to be made during run 0 Runtime for the run 0 ps Run end step 0 Run end time 0 ps Extending remaining runtime by 100 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 100000 Runtime for the run 100 ps Run end step 100000 Run end time 100 ps Input file: Run start step 0 Run start time 0 ps Step to be made during run 100000 Runtime for the run 100 ps Run end step 100000 Run end time 100 ps Extending remaining runtime by 100 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 200000 Runtime for the run 200 ps Run end step 200000 Run end time 200 ps [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (142 ms) [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2022 (single precision) Setting the LD random seed to -69484562 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data Input file: Run start step 0 Run start time 0 ps Step to be made during run 0 Runtime for the run 0 ps Run end step 0 Run end time 0 ps Extending remaining runtime to 100 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 100000 Runtime for the run 100 ps Run end step 100000 Run end time 100 ps [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (139 ms) [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file lysozyme.top, line 1465]: System has non-zero total charge: 2.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 465.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022 (single precision) Setting nsteps to 102 Reading file ${WORKDIR}/gromacs-2022/build/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2022 (single precision) Setting the LD random seed to -553913345 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Analysing residue names: There are: 10 Protein residues Analysing Protein... This run will generate roughly 0 Mb of data Input file: Run start step 0 Run start time 0 ps Step to be made during run 0 Runtime for the run 0 ps Run end step 0 Run end time 0 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 102 Runtime for the run 0.102 ps Run end step 102 Run end time 0.102 ps [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (138 ms) [----------] 3 tests from ConvertTprTest (421 ms total) [----------] 12 tests from Works/TrjconvWithDifferentInputFormats [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: trr version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (6 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (5 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (5 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (5 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (5 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (6 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (4 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (4 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (4 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (4 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (4 ms) [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 Will write trr: Trajectory in portable xdr format Group 0 ( System) has 6 elements Group 1 (FirstWaterMolecule) has 3 elements Group 2 (SecondWaterMolecule) has 3 elements Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 -> frame 1 time 1.000 Last written: frame 1 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 2: 'SecondWaterMolecule' [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (5 ms) [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (62 ms total) [----------] 30 tests from Works/TrjconvDumpTest [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 Precision of ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 'Generated by trjconv t= 1.00000 step= 1', 6 atoms Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (2 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (3 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (3 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 0 ps -> frame 0 time 0.000 Last written: frame 0 time 0.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (4 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (3 ms) [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 Will write trr: Trajectory in portable xdr format Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 Dumping frame at t= 1 ps -> frame 0 time 1.000 Last written: frame 0 time 1.000 Note that major changes are planned in future for trjconv, to improve usability and utility. [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (3 ms) [----------] 30 tests from Works/TrjconvDumpTest (89 ms total) [----------] Global test environment tear-down [==========] 54 tests from 6 test suites ran. (855 ms total) [ PASSED ] 54 tests. Test time = 1.55 sec ---------------------------------------------------------- Test Passed. "ToolUnitTests" end time: Feb 22 23:22 EST "ToolUnitTests" time elapsed: 00:00:01 ---------------------------------------------------------- 60/90 Testing: FileIOTests 60/90 Test: FileIOTests Command: "${WORKDIR}/gromacs-2022/build/bin/fileio-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/FileIOTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/fileio/tests "FileIOTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 42 tests from 10 test suites. [----------] Global test environment set-up. [----------] 4 tests from Checkpoint [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) [ RUN ] Checkpoint.KvtRoundTripInt64 [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) [ RUN ] Checkpoint.KvtRoundTripReal [ OK ] Checkpoint.KvtRoundTripReal (0 ms) [----------] 4 tests from Checkpoint (0 ms total) [----------] 2 tests from FileMD5Test [ RUN ] FileMD5Test.CanComputeMD5 [ OK ] FileMD5Test.CanComputeMD5 (2 ms) [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) [----------] 2 tests from FileMD5Test (3 ms total) [----------] 3 tests from MrcSerializer [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) [----------] 3 tests from MrcSerializer (0 ms total) [----------] 4 tests from MrcDensityMap [ RUN ] MrcDensityMap.RoundTripIsIdempotent [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms) [ RUN ] MrcDensityMap.ReadsDensityDataFromFile [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) [----------] 4 tests from MrcDensityMap (3 ms total) [----------] 8 tests from MrcDensityMapHeaderTest [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) [ RUN ] MrcDensityMapHeaderTest.IsSane [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) [----------] 10 tests from ReadTest [ RUN ] ReadTest.get_eint_ReadsInteger [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) [ RUN ] ReadTest.get_eint_WarnsAboutFloat ERROR 1 [file unknown, line 0]: Right hand side '0.8' for parameter 'test' in parameter file is not an integer value [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) [ RUN ] ReadTest.get_eint_WarnsAboutString ERROR 1 [file unknown, line 0]: Right hand side 'hello' for parameter 'test' in parameter file is not an integer value [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) [ RUN ] ReadTest.get_eint64_ReadsInteger [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) [ RUN ] ReadTest.get_eint64_WarnsAboutFloat ERROR 1 [file unknown, line 0]: Right hand side '0.8' for parameter 'test' in parameter file is not an integer value [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) [ RUN ] ReadTest.get_eint64_WarnsAboutString ERROR 1 [file unknown, line 0]: Right hand side 'hello' for parameter 'test' in parameter file is not an integer value [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) [ RUN ] ReadTest.get_ereal_ReadsInteger [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) [ RUN ] ReadTest.get_ereal_ReadsFloat [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) [ RUN ] ReadTest.get_ereal_WarnsAboutString ERROR 1 [file unknown, line 0]: Right hand side 'hello' for parameter 'test' in parameter file is not a real value [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) [----------] 10 tests from ReadTest (0 ms total) [----------] 1 test from FileIOXdrSerializerTest [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) [----------] 1 test from FileIOXdrSerializerTest (1 ms total) [----------] 2 tests from TngTest [ RUN ] TngTest.CanOpenTngFile TNG library: Cannot open file spc2-traj.tng. ${WORKDIR}/gromacs-2022/src/external/tng_io/src/lib/tng_io.c: 890 TNG library: Cannot open file spc2-traj.tng. ${WORKDIR}/gromacs-2022/src/external/tng_io/src/lib/tng_io.c: 890 [ OK ] TngTest.CanOpenTngFile (0 ms) [ RUN ] TngTest.CloseBeforeOpenIsNotFatal [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) [----------] 2 tests from TngTest (0 ms total) [----------] 4 tests from XvgioTest [ RUN ] XvgioTest.readXvgIntWorks [ OK ] XvgioTest.readXvgIntWorks (1 ms) [ RUN ] XvgioTest.readXvgRealWorks [ OK ] XvgioTest.readXvgRealWorks (1 ms) [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (1 ms) [ RUN ] XvgioTest.readXvgDeprecatedWorks [ OK ] XvgioTest.readXvgDeprecatedWorks (1 ms) [----------] 4 tests from XvgioTest (5 ms total) [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms) [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms) [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (3 ms) [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms) [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (13 ms total) [----------] Global test environment tear-down [==========] 42 tests from 10 test suites ran. (28 ms total) [ PASSED ] 42 tests. Test time = 0.71 sec ---------------------------------------------------------- Test Passed. "FileIOTests" end time: Feb 22 23:22 EST "FileIOTests" time elapsed: 00:00:00 ---------------------------------------------------------- 61/90 Testing: SelectionUnitTests 61/90 Test: SelectionUnitTests Command: "${WORKDIR}/gromacs-2022/build/bin/selection-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/SelectionUnitTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/gromacs/selection/tests "SelectionUnitTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 201 tests from 11 test suites. [----------] Global test environment set-up. [----------] 1 test from IndexGroupTest [ RUN ] IndexGroupTest.RemovesDuplicates [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) [----------] 1 test from IndexGroupTest (0 ms total) [----------] 15 tests from IndexBlockTest [ RUN ] IndexBlockTest.CreatesUnknownBlock [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) [ RUN ] IndexBlockTest.CreatesAtomBlock [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) [ RUN ] IndexBlockTest.CreatesSingleBlock [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) [----------] 15 tests from IndexBlockTest (5 ms total) [----------] 11 tests from IndexMapTest [ RUN ] IndexMapTest.InitializesAtomBlock [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) [ RUN ] IndexMapTest.InitializesOrgIdGroupAll [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) [ RUN ] IndexMapTest.InitializesMoleculeBlock [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) [ RUN ] IndexMapTest.MapsSingleBlock [ OK ] IndexMapTest.MapsSingleBlock (0 ms) [ RUN ] IndexMapTest.MapsResidueBlocks [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) [ RUN ] IndexMapTest.MapsResidueBlocksWithMask [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) [ RUN ] IndexMapTest.HandlesMultipleRequests [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) [----------] 11 tests from IndexMapTest (6 ms total) [----------] 3 tests from IndexGroupsAndNamesTest [ RUN ] IndexGroupsAndNamesTest.containsNames [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) [----------] 15 tests from NeighborhoodSearchTest [ RUN ] NeighborhoodSearchTest.SimpleSearch [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) [ RUN ] NeighborhoodSearchTest.SimpleSearchXY [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) [ RUN ] NeighborhoodSearchTest.GridSearchBox [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) [ RUN ] NeighborhoodSearchTest.GridSearchXYBox [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (21 ms) [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) [ RUN ] NeighborhoodSearchTest.HandlesNoPBC [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) [ RUN ] NeighborhoodSearchTest.HandlesNullPBC [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) [ RUN ] NeighborhoodSearchTest.GridSearchExclusions [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) [----------] 15 tests from NeighborhoodSearchTest (51 ms total) [----------] 13 tests from PositionCalculationTest [ RUN ] PositionCalculationTest.ComputesAtomPositions [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) [ RUN ] PositionCalculationTest.ComputesPositionMask [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) [----------] 13 tests from PositionCalculationTest (8 ms total) [----------] 33 tests from SelectionCollectionTest [ RUN ] SelectionCollectionTest.HandlesNoSelections [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) [ RUN ] SelectionCollectionTest.RetrieveValidSelection [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) [----------] 33 tests from SelectionCollectionTest (22 ms total) [----------] 14 tests from SelectionCollectionInteractiveTest [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) [----------] 14 tests from SelectionCollectionInteractiveTest (13 ms total) [----------] 70 tests from SelectionCollectionDataTest [ RUN ] SelectionCollectionDataTest.HandlesAllNone [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesAtomnr [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesResnr [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesResIndex [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesMolIndex [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesAtomname [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesAtomtype [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesChain [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesMass [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesCharge [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesAltLoc [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesInsertCode [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesOccupancy [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesBeta [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesResname [ OK ] SelectionCollectionDataTest.HandlesResname (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesSameResidue [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (3 ms) [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (2 ms) [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (2 ms) [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (2 ms) [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (2 ms) [----------] 70 tests from SelectionCollectionDataTest (125 ms total) [----------] 17 tests from SelectionOptionTest [ RUN ] SelectionOptionTest.ParsesSimpleSelection [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) [ RUN ] SelectionOptionTest.ChecksEmptySelections [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) [ RUN ] SelectionOptionTest.HandlesTooManySelections [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) [ RUN ] SelectionOptionTest.HandlesTooFewSelections [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) [ RUN ] SelectionOptionTest.HandlesAdjuster [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) [----------] 17 tests from SelectionOptionTest (4 ms total) [----------] 9 tests from SelectionFileOptionTest [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) [----------] 9 tests from SelectionFileOptionTest (4 ms total) [----------] Global test environment tear-down [==========] 201 tests from 11 test suites ran. (243 ms total) [ PASSED ] 201 tests. Test time = 0.91 sec ---------------------------------------------------------- Test Passed. "SelectionUnitTests" end time: Feb 22 23:22 EST "SelectionUnitTests" time elapsed: 00:00:00 ---------------------------------------------------------- 62/90 Testing: ParserTest 62/90 Test: ParserTest Command: "${WORKDIR}/gromacs-2022/build/bin/t_ParserTest" Directory: ${WORKDIR}/gromacs-2022/build/_deps/muparser-build "ParserTest" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- testing name restriction enforcement...passed testing syntax engine...passed testing postfix operators...passed testing infix operators...passed testing variable/constant detection...passed testing multiarg functions...passed testing expression samples...passed testing if-then-else operator...passed testing member functions...passed testing binary operators...passed testing error codes...passed testing string arguments...passed testing bulkmode...passed Test passed (569 expressions) Test time = 0.05 sec ---------------------------------------------------------- Test Passed. "ParserTest" end time: Feb 22 23:22 EST "ParserTest" time elapsed: 00:00:00 ---------------------------------------------------------- 63/90 Testing: MdrunOutputTests 63/90 Test: MdrunOutputTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-output-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunOutputTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunOutputTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 12 tests from 5 test suites. [----------] Global test environment set-up. [----------] 1 test from MdrunTest [ RUN ] MdrunTest.WritesHelp [ OK ] MdrunTest.WritesHelp (45 ms) [----------] 1 test from MdrunTest (45 ms total) [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 1 steps, 0.0 ps. Setting the LD random seed to -1073954 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 6.217 3.109 200.0 (ns/day) (hour/ns) Performance: 0.056 431.772 Reading frame 0 time 0.000 # Atoms 6 Reading frame 1 time 0.001 Last frame 1 time 0.001 Item #frames Timestep (ps) Step 2 0.001 Time 2 0.001 Lambda 0 Coords 2 0.001 Velocities 0 Forces 0 Box 2 0.001 Checking file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (3249 ms) [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 1 steps, 0.0 ps. Setting the LD random seed to -268436481 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.665 0.333 199.9 (ns/day) (hour/ns) Performance: 0.519 46.248 Reading frame 0 time 0.000 # Atoms 6 Reading frame 1 time 0.001 Last frame 1 time 0.001 Item #frames Timestep (ps) Step 2 0.001 Time 2 0.001 Lambda 0 Coords 2 0.001 Velocities 0 Forces 0 Box 2 0.001 Checking file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (462 ms) [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 1 steps, 0.0 ps. Setting the LD random seed to -705217033 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.323 1.662 200.0 (ns/day) (hour/ns) Performance: 0.104 230.776 Reading frame 0 time 0.000 # Atoms 3 Reading frame 1 time 0.001 Last frame 1 time 0.001 Item #frames Timestep (ps) Step 2 0.001 Time 2 0.001 Lambda 0 Coords 2 0.001 Velocities 0 Forces 0 Box 2 0.001 Checking file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (1786 ms) [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (5498 ms total) [----------] 2 tests from Argon12/OutputFiles [ RUN ] Argon12/OutputFiles.FilesArePresent/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.569 2.285 200.0 (ns/day) (hour/ns) Performance: 0.643 37.332 [ OK ] Argon12/OutputFiles.FilesArePresent/0 (2386 ms) [ RUN ] Argon12/OutputFiles.FilesArePresent/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 12.465 6.232 200.0 (ns/day) (hour/ns) Performance: 0.236 101.835 [ OK ] Argon12/OutputFiles.FilesArePresent/1 (6299 ms) [----------] 2 tests from Argon12/OutputFiles (8685 ms total) [----------] 3 tests from MdrunCanWrite/Trajectories [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 6 steps, 0.0 ps. Setting the LD random seed to -1361388618 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 12.653 6.327 200.0 (ns/day) (hour/ns) Performance: 0.096 251.057 [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (6460 ms) [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 6 steps, 0.0 ps. Setting the LD random seed to -5554211 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.986 0.993 200.0 (ns/day) (hour/ns) Performance: 0.609 39.418 [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (1124 ms) [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 6 steps, 0.0 ps. Setting the LD random seed to -18358469 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.873 0.937 200.0 (ns/day) (hour/ns) Performance: 0.646 37.176 [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (1073 ms) [----------] 3 tests from MdrunCanWrite/Trajectories (8658 ms total) [----------] 3 tests from MdrunCanWrite/NptTrajectories [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 2 steps, 0.0 ps. Setting the LD random seed to 2045468622 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.992 0.496 199.9 (ns/day) (hour/ns) Performance: 0.523 45.916 [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (637 ms) [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 2 steps, 0.0 ps. Setting the LD random seed to -537985657 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.094 0.547 200.0 (ns/day) (hour/ns) Performance: 0.474 50.664 [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (683 ms) [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 Number of degrees of freedom in T-Coupling group System is 12.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 2 steps, 0.0 ps. Setting the LD random seed to -117894657 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.958 0.479 200.0 (ns/day) (hour/ns) Performance: 0.541 44.345 [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (611 ms) [----------] 3 tests from MdrunCanWrite/NptTrajectories (1932 ms total) [----------] Global test environment tear-down [==========] 12 tests from 5 test suites ran. (25027 ms total) [ PASSED ] 12 tests. Test time = 25.70 sec ---------------------------------------------------------- Test Passed. "MdrunOutputTests" end time: Feb 22 23:22 EST "MdrunOutputTests" time elapsed: 00:00:25 ---------------------------------------------------------- 64/90 Testing: MdrunModulesTests 64/90 Test: MdrunModulesTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-modules-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunModulesTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunModulesTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 15 tests from 3 test suites. [----------] Global test environment set-up. [----------] 9 tests from DensityFittingTest [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct Number of degrees of freedom in T-Coupling group rest is 33.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = -3.8565400e+03 Maximum force = 2.8846870e+03 on atom 3 Norm of force = 1.0754448e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -675129886 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (329 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation Number of degrees of freedom in T-Coupling group rest is 33.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = -9.8208447e+03 Maximum force = 4.7331094e+03 on atom 2 Norm of force = 1.7801224e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -201329045 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (340 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (1 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix Number of degrees of freedom in T-Coupling group rest is 33.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = -9.7604385e+03 Maximum force = 4.6344800e+03 on atom 2 Norm of force = 1.7575605e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1078203009 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (343 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (2 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix Number of degrees of freedom in T-Coupling group rest is 33.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = -3.8565400e+03 Maximum force = 2.8846870e+03 on atom 3 Norm of force = 1.0754448e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1748029057 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (328 ms) [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy Number of degrees of freedom in T-Coupling group rest is 33.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = -2.7138666e+04 Maximum force = 4.3409717e+03 on atom 2 Norm of force = 1.2549793e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -833421378 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (329 ms) [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (1 ms) [ RUN ] DensityFittingTest.CheckpointWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (2) Number of degrees of freedom in T-Coupling group rest is 33.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 2 steps, 0.0 ps. Setting the LD random seed to 805174271 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.979 0.496 197.5 (ns/day) (hour/ns) Performance: 0.523 45.881 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.093 0.547 199.9 (ns/day) (hour/ns) Performance: 0.790 30.365 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (1203 ms) [----------] 9 tests from DensityFittingTest (2881 ms total) [----------] 4 tests from MimicTest [ RUN ] MimicTest.OneQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 49 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.196 0.098 199.6 (ns/day) (hour/ns) Performance: 0.879 27.303 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 930968291 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' This run will generate roughly 0 Mb of data [ OK ] MimicTest.OneQuantumMol (151 ms) [ RUN ] MimicTest.AllQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 45 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.182 0.091 199.6 (ns/day) (hour/ns) Performance: 0.948 25.311 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2006966615 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' This run will generate roughly 0 Mb of data [ OK ] MimicTest.AllQuantumMol (141 ms) [ RUN ] MimicTest.TwoQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 40 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.198 0.099 199.6 (ns/day) (hour/ns) Performance: 0.872 27.509 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -149160138 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' This run will generate roughly 0 Mb of data [ OK ] MimicTest.TwoQuantumMol (149 ms) [ RUN ] MimicTest.BondCuts NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 66.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: NVE simulation: will use the initial temperature of 300.368 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/ala.gro' Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 NOTE: 36 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.235 0.118 199.7 (ns/day) (hour/ns) Performance: 0.735 32.650 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -537105551 Generated 2211 of the 2211 non-bonded parameter combinations Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] MimicTest.BondCuts (188 ms) [----------] 4 tests from MimicTest (631 ms total) [----------] 2 tests from WithIntegrator/ImdTest [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 Generating 1-4 interactions: fudge = 1 NOTE 1 [file glycine_vacuo.top, line 12]: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads IMD: Enabled. This simulation will accept incoming IMD connections. IMD: Pulling from IMD remote is enabled (-imdpull). IMD: Setting port for connection requests to 0. IMD: Setting up incoming socket. IMD: Listening for IMD connection on port 32841. IMD: -imdwait not set, starting simulation. starting mdrun 'Glycine' 2 steps, 0.0 ps. Setting the LD random seed to 1072627703 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.925 0.463 199.9 (ns/day) (hour/ns) Performance: 1.121 21.416 [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (621 ms) [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not apply to steep. Generating 1-4 interactions: fudge = 1 Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads IMD: Enabled. This simulation will accept incoming IMD connections. IMD: Pulling from IMD remote is enabled (-imdpull). IMD: Setting port for connection requests to 0. IMD: Setting up incoming socket. IMD: Listening for IMD connection on port 58843. IMD: -imdwait not set, starting simulation. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 3 steps. Potential Energy = 1.1977062e+03 Maximum force = 1.7794875e+04 on atom 9 Norm of force = 7.8732895e+03 Setting the LD random seed to -16781217 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' This run will generate roughly 0 Mb of data [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (533 ms) [----------] 2 tests from WithIntegrator/ImdTest (1154 ms total) [----------] Global test environment tear-down [==========] 15 tests from 3 test suites ran. (4800 ms total) [ PASSED ] 15 tests. Test time = 5.50 sec ---------------------------------------------------------- Test Passed. "MdrunModulesTests" end time: Feb 22 23:22 EST "MdrunModulesTests" time elapsed: 00:00:05 ---------------------------------------------------------- 65/90 Testing: MdrunIOTests 65/90 Test: MdrunIOTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-io-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunIOTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunIOTests" start time: Feb 22 23:22 EST Output: ---------------------------------------------------------- [==========] Running 67 tests from 12 test suites. [----------] Global test environment set-up. [----------] 5 tests from GromppTest [ RUN ] GromppTest.EmptyMdpFileWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Setting the LD random seed to -1145207049 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.EmptyMdpFileWorks (12 ms) [ RUN ] GromppTest.SimulatedAnnealingWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Simulated annealing for group rest: Periodic, 4 timepoints Time (ps) Temperature (K) 0.0 298.0 2.0 320.0 4.0 320.0 6.0 298.0 Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Setting the LD random seed to -36460801 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.SimulatedAnnealingWorks (9 ms) [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Simulated annealing for group Methanol: Single, 3 timepoints Time (ps) Temperature (K) 0.0 298.0 3.0 280.0 6.0- 270.0 Simulated annealing for group SOL: Periodic, 4 timepoints Time (ps) Temperature (K) 0.0 298.0 2.0 320.0 4.0 320.0 6.0 298.0 Number of degrees of freedom in T-Coupling group Methanol is 7.20 Number of degrees of freedom in T-Coupling group SOL is 4.80 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Setting the LD random seed to 804724156 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (10 ms) [ RUN ] GromppTest.ValidTransformationCoord NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Pull group 1 'SOL' has 3 atoms Pull group 2 'Methanol' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 3 5 2 3 2 0.613 nm 0.000 nm 1 3 5 2 3 2 0.613 nm 0.000 nm There were 3 notes Setting the LD random seed to 2145335097 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] GromppTest.ValidTransformationCoord (2155 ms) [ RUN ] GromppTest.InvalidTransformationCoord NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Pull group 1 'SOL' has 3 atoms Pull group 2 'Methanol' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 12.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Pull group natoms pbc atom distance at start reference at t=0 1 3 5 2 3 2 0.613 nm 0.000 nm 1 3 5 2 3 2 Setting the LD random seed to -608708033 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm Note that mdrun will redetermine rlist based on the actual pair-list setup [ OK ] GromppTest.InvalidTransformationCoord (1580 ms) [----------] 5 tests from GromppTest (3768 ms total) [----------] 6 tests from MdrunTerminationTest [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -403083270 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.652 1.826 200.0 (ns/day) (hour/ns) Performance: 0.142 169.112 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.696 0.348 199.9 (ns/day) (hour/ns) Performance: 0.745 32.213 [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (2349 ms) [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 1.024 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 100 steps, 0.1 ps. Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps Setting the LD random seed to -923504745 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE: 26 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.727 0.364 199.9 (ns/day) (hour/ns) Performance: 0.475 50.514 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022 (single precision) Setting nsteps to 102 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 100 Runtime for the run 0.1 ps Run end step 100 Run end time 0.1 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 102 Runtime for the run 0.102 ps Run end step 102 Run end time 0.102 ps Writing final coordinates. Core t (s) Wall t (s) (%) Time: 17.821 8.911 200.0 (ns/day) (hour/ns) Performance: 0.989 24.266 [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (9442 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -555361569 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.804 0.402 199.9 (ns/day) (hour/ns) Performance: 0.645 37.231 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.389 2.195 200.0 (ns/day) (hour/ns) Performance: 0.118 203.222 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Setting nsteps to 6 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 6 Runtime for the run 0.006 ps Run end step 6 Run end time 0.006 ps Writing final coordinates. NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.729 0.365 199.9 (ns/day) (hour/ns) Performance: 0.711 33.766 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Setting nsteps to 8 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 6 Runtime for the run 0.006 ps Run end step 6 Run end time 0.006 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 8 Runtime for the run 0.008 ps Run end step 8 Run end time 0.008 ps Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.695 0.348 199.9 (ns/day) (hour/ns) Performance: 0.745 32.197 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.273 0.137 199.8 (ns/day) (hour/ns) Performance: 0.633 37.944 [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (3765 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1639973025 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.812 0.406 199.9 (ns/day) (hour/ns) Performance: 0.638 37.601 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps. Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.167 0.584 200.0 (ns/day) (hour/ns) Performance: 0.740 32.419 [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (1223 ms) [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -134222603 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.821 0.411 199.9 (ns/day) (hour/ns) Performance: 0.631 38.042 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (535 ms) [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1610613059 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.799 0.400 199.5 (ns/day) (hour/ns) Performance: 0.647 37.075 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022 (single precision) Setting nsteps to 4 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Input file: Run start step 0 Run start time 0 ps Step to be made during run 2 Runtime for the run 0.002 ps Run end step 2 Run end time 0.002 ps Output file: Run start step 0 Run start time 0 ps Step to be made during run 4 Runtime for the run 0.004 ps Run end step 4 Run end time 0.004 ps Writing final coordinates. NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.786 0.393 199.9 (ns/day) (hour/ns) Performance: 0.659 36.400 [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (965 ms) [----------] 6 tests from MdrunTerminationTest (18281 ms total) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 7.418 3.709 200.0 (ns/day) (hour/ns) Performance: 0.396 60.609 trr version: GMX_trn_file (single precision) [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (3820 ms) [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.631 2.315 200.0 (ns/day) (hour/ns) Performance: 0.634 37.833 [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (2378 ms) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (6199 ms total) [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.255 1.634 199.2 (ns/day) (hour/ns) Performance: 0.899 26.695 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.848 0.924 200.0 (ns/day) (hour/ns) Performance: 0.841 28.528 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.839 0.920 200.0 (ns/day) (hour/ns) Performance: 0.845 28.390 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (3726 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.519 2.259 200.0 (ns/day) (hour/ns) Performance: 0.650 36.917 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.136 1.068 200.0 (ns/day) (hour/ns) Performance: 0.728 32.963 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.138 1.069 200.0 (ns/day) (hour/ns) Performance: 0.728 32.989 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (4571 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 76.990 38.495 200.0 (ns/day) (hour/ns) Performance: 0.038 629.007 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.016 2.008 200.0 (ns/day) (hour/ns) Performance: 0.387 61.986 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.777 0.889 199.9 (ns/day) (hour/ns) Performance: 0.875 27.433 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (41646 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.263 1.632 200.0 (ns/day) (hour/ns) Performance: 0.900 26.664 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5.164 2.582 200.0 (ns/day) (hour/ns) Performance: 0.301 79.698 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 10.187 5.094 200.0 (ns/day) (hour/ns) Performance: 0.153 157.218 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (9555 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 9.677 4.839 200.0 (ns/day) (hour/ns) Performance: 0.304 79.068 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.092 1.049 199.5 (ns/day) (hour/ns) Performance: 0.741 32.367 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.082 1.041 200.0 (ns/day) (hour/ns) Performance: 0.747 32.142 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (7232 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 13.550 6.775 200.0 (ns/day) (hour/ns) Performance: 0.217 110.703 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 15.486 7.743 200.0 (ns/day) (hour/ns) Performance: 0.100 238.979 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.653 1.326 200.0 (ns/day) (hour/ns) Performance: 0.586 40.937 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (16028 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 7.311 3.656 200.0 (ns/day) (hour/ns) Performance: 0.402 59.736 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.268 2.134 200.0 (ns/day) (hour/ns) Performance: 0.364 65.877 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.845 1.923 200.0 (ns/day) (hour/ns) Performance: 0.404 59.337 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (7972 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Test time = 120.04 sec ---------------------------------------------------------- Test Failed. "MdrunIOTests" end time: Feb 22 23:24 EST "MdrunIOTests" time elapsed: 00:02:00 ---------------------------------------------------------- 66/90 Testing: MdrunTestsOneRank 66/90 Test: MdrunTestsOneRank Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "1" "${WORKDIR}/gromacs-2022/build/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunTestsOneRank.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunTestsOneRank" start time: Feb 22 23:24 EST Output: ---------------------------------------------------------- [==========] Running 26 tests from 6 test suites. [----------] Global test environment set-up. [----------] 1 test from CompelTest [ RUN ] CompelTest.SwapCanRun Setting the LD random seed to -1111777549 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'OCT' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'OCT' Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Split0 group 'Ch0' contains 83 atoms. Split1 group 'Ch1' contains 83 atoms. Solvent group 'SOL' contains 11931 atoms. Swap group 'NA+' contains 19 atoms. Swap group 'CL-' contains 19 atoms. Number of degrees of freedom in T-Coupling group System is 27869.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 1 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022 (single precision) GPU direct communication can not be activated because: Swap-coords is not supported. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads SWAP: Determining initial numbers of ions per compartment. SWAP: Setting pointers for checkpoint writing SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules starting mdrun 'Channel_coco in octane membrane' 2 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.429 0.715 199.9 (ns/day) (hour/ns) Performance: 1.813 13.238 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps GPU direct communication can not be activated because: Swap-coords is not supported. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads SWAP: Setting pointers for checkpoint writing SWAP: Copying channel fluxes from checkpoint file data SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules starting mdrun 'Channel_coco in octane membrane' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.341 0.171 199.7 (ns/day) (hour/ns) Performance: 7.591 3.162 [ OK ] CompelTest.SwapCanRun (1137 ms) [----------] 1 test from CompelTest (1137 ms total) [----------] 6 tests from BondedInteractionsTest [ RUN ] BondedInteractionsTest.NormalBondWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -807436311 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: In moleculetype 'butane' 2 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 167.0 (ns/day) (hour/ns) Performance: 78.490 0.306 [ OK ] BondedInteractionsTest.NormalBondWorks (26 ms) [ RUN ] BondedInteractionsTest.TabulatedBondWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -671154283 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: In moleculetype 'butane' 2 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 165.6 (ns/day) (hour/ns) Performance: 86.883 0.276 [ OK ] BondedInteractionsTest.TabulatedBondWorks (15 ms) [ RUN ] BondedInteractionsTest.NormalAngleWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -1245184289 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 164.0 (ns/day) (hour/ns) Performance: 88.001 0.273 [ OK ] BondedInteractionsTest.NormalAngleWorks (13 ms) [ RUN ] BondedInteractionsTest.TabulatedAngleWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -403708182 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 163.7 (ns/day) (hour/ns) Performance: 89.434 0.268 [ OK ] BondedInteractionsTest.TabulatedAngleWorks (16 ms) [ RUN ] BondedInteractionsTest.NormalDihedralWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -100830737 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 164.3 (ns/day) (hour/ns) Performance: 87.175 0.275 [ OK ] BondedInteractionsTest.NormalDihedralWorks (13 ms) [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -4261893 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.002 0.001 163.8 (ns/day) (hour/ns) Performance: 84.809 0.283 [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (15 ms) [----------] 6 tests from BondedInteractionsTest (101 ms total) [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 Setting the LD random seed to -275284099 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.601 1.301 200.0 (ns/day) (hour/ns) Performance: 0.332 72.274 Setting the LD random seed to -1107300677 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.048 0.024 198.4 (ns/day) (hour/ns) Performance: 17.835 1.346 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1782 ms) [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 Setting the LD random seed to -311972421 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.062 0.031 198.6 (ns/day) (hour/ns) Performance: 13.741 1.747 Setting the LD random seed to 2045705975 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.058 0.029 198.6 (ns/day) (hour/ns) Performance: 14.836 1.618 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (106 ms) [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1888 ms total) [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 Setting the LD random seed to 1559882675 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 9.00 Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.107 0.054 198.7 (ns/day) (hour/ns) Performance: 8.014 2.995 Setting the LD random seed to -136585473 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 9.00 Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 4 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.064 0.033 197.8 (ns/day) (hour/ns) Performance: 13.249 1.811 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (118 ms) [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (118 ms total) [----------] 12 tests from FreezeWorks/FreezeGroupTest [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.055 0.028 198.5 (ns/day) (hour/ns) Performance: 28.004 0.857 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (50 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.041 0.020 198.0 (ns/day) (hour/ns) Performance: 38.004 0.632 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (39 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.098 0.049 199.2 (ns/day) (hour/ns) Performance: 15.860 1.513 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (68 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.063 0.032 198.7 (ns/day) (hour/ns) Performance: 24.659 0.973 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (50 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.016 197.6 (ns/day) (hour/ns) Performance: 48.003 0.500 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (35 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/freezegroups.cpp:194: Skipped Parrinello-Rahman is not implemented in md-vv. [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.461 0.231 199.8 (ns/day) (hour/ns) Performance: 3.373 7.115 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (251 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.931 2.466 200.0 (ns/day) (hour/ns) Performance: 0.315 76.105 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (2487 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.076 0.038 199.0 (ns/day) (hour/ns) Performance: 20.363 1.179 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (62 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.092 0.046 199.2 (ns/day) (hour/ns) Performance: 16.837 1.425 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (67 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.088 0.044 197.6 (ns/day) (hour/ns) Performance: 17.479 1.373 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (65 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.140 0.070 199.4 (ns/day) (hour/ns) Performance: 11.109 2.160 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (91 ms) [----------] 12 tests from FreezeWorks/FreezeGroupTest (3271 ms total) [----------] 4 tests from AccelerationWorks/AccelerationGroupTest [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -167908097 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 34.393 17.197 200.0 (ns/day) (hour/ns) Performance: 0.090 265.385 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (17214 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -33621281 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because verlet-buffer-tolerance is not set or used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 13.711 6.856 200.0 (ns/day) (hour/ns) Performance: 0.227 105.797 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (6874 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -134906039 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.311 0.156 199.8 (ns/day) (hour/ns) Performance: 9.973 2.406 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (175 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -67250242 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because verlet-buffer-tolerance is not set or used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.106 0.053 199.3 (ns/day) (hour/ns) Performance: 29.229 0.821 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (67 ms) [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (24331 ms total) [----------] Global test environment tear-down [==========] 26 tests from 6 test suites ran. (31134 ms total) [ PASSED ] 25 tests. [ SKIPPED ] 1 test, listed below: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 Test time = 31.83 sec ---------------------------------------------------------- Test Passed. "MdrunTestsOneRank" end time: Feb 22 23:25 EST "MdrunTestsOneRank" time elapsed: 00:00:31 ---------------------------------------------------------- 67/90 Testing: MdrunTestsTwoRanks 67/90 Test: MdrunTestsTwoRanks Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunTestsTwoRanks.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunTestsTwoRanks" start time: Feb 22 23:25 EST Output: ---------------------------------------------------------- [==========] Running 26 tests from 6 test suites. [----------] Global test environment set-up. [----------] 1 test from CompelTest [ RUN ] CompelTest.SwapCanRun Setting the LD random seed to -205263186 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'OCT' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'OCT' Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Split0 group 'Ch0' contains 83 atoms. Split1 group 'Ch1' contains 83 atoms. Solvent group 'SOL' contains 11931 atoms. Swap group 'NA+' contains 19 atoms. Swap group 'CL-' contains 19 atoms. Number of degrees of freedom in T-Coupling group System is 27869.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 1 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022 (single precision) GPU direct communication can not be activated because: Swap-coords is not supported. Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process SWAP: Determining initial numbers of ions per compartment. SWAP: Setting pointers for checkpoint writing SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules starting mdrun 'Channel_coco in octane membrane' 2 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.8%. The balanceable part of the MD step is 20%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. Core t (s) Wall t (s) (%) Time: 11.274 2.819 399.9 (ns/day) (hour/ns) Performance: 0.460 52.200 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps GPU direct communication can not be activated because: Swap-coords is not supported. Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process SWAP: Setting pointers for checkpoint writing SWAP: Copying channel fluxes from checkpoint file data SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules starting mdrun 'Channel_coco in octane membrane' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.442 0.111 399.1 (ns/day) (hour/ns) Performance: 11.693 2.053 [ OK ] CompelTest.SwapCanRun (3182 ms) [----------] 1 test from CompelTest (3182 ms total) [----------] 6 tests from BondedInteractionsTest [ RUN ] BondedInteractionsTest.NormalBondWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -1082134021 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: In moleculetype 'butane' 2 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 338.7 (ns/day) (hour/ns) Performance: 71.995 0.333 [ OK ] BondedInteractionsTest.NormalBondWorks (34 ms) [ RUN ] BondedInteractionsTest.TabulatedBondWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -1265172610 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: In moleculetype 'butane' 2 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 336.1 (ns/day) (hour/ns) Performance: 79.072 0.304 [ OK ] BondedInteractionsTest.TabulatedBondWorks (17 ms) [ RUN ] BondedInteractionsTest.NormalAngleWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 2126507135 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 334.8 (ns/day) (hour/ns) Performance: 78.977 0.304 [ OK ] BondedInteractionsTest.NormalAngleWorks (15 ms) [ RUN ] BondedInteractionsTest.TabulatedAngleWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -139561 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 333.6 (ns/day) (hour/ns) Performance: 80.719 0.297 [ OK ] BondedInteractionsTest.TabulatedAngleWorks (18 ms) [ RUN ] BondedInteractionsTest.NormalDihedralWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -436899857 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 339.3 (ns/day) (hour/ns) Performance: 74.881 0.321 [ OK ] BondedInteractionsTest.NormalDihedralWorks (16 ms) [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -281554945 Generated 3 of the 3 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'butane' NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: In moleculetype 'butane' 4 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'A single butane', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/butane1.gro' Reading frames from gro file 'A single butane', 4 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 336.5 (ns/day) (hour/ns) Performance: 77.807 0.308 [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (18 ms) [----------] 6 tests from BondedInteractionsTest (121 ms total) [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 Setting the LD random seed to -405146523 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 12.232 3.058 400.0 (ns/day) (hour/ns) Performance: 0.141 169.909 Setting the LD random seed to 2147196900 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.311 0.328 399.7 (ns/day) (hour/ns) Performance: 1.317 18.219 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) trr version: GMX_trn_file (single precision) Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (3839 ms) [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 Setting the LD random seed to 2145271775 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 76.741 19.185 400.0 (ns/day) (hour/ns) Performance: 0.023 1065.858 Setting the LD random seed to 2113879727 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... NOTE 1 [file ala.top, line 256]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 54.00 The largest distance between excluded atoms is 0.384 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 Estimate for the relative computational load of the PME mesh part: 0.95 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'UNNAMED in water' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.173 0.043 398.1 (ns/day) (hour/ns) Performance: 9.939 2.415 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Last energy frame read 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (19280 ms) [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (23120 ms total) [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 Setting the LD random seed to -5594114 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 9.00 Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 2.437 0.610 399.8 (ns/day) (hour/ns) Performance: 0.709 33.868 Setting the LD random seed to -566831169 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group rest is 9.00 Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 1.112 nm 1.000 nm This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. Can not increase nstlist because an NVE ensemble is used GPU direct communication can not be activated because: MTS is not supported. Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 4 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 5.629 1.408 399.9 (ns/day) (hour/ns) Performance: 0.307 78.198 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2053 ms) [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2053 ms total) [----------] 12 tests from FreezeWorks/FreezeGroupTest [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.3%. The balanceable part of the MD step is 33%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.4%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.412 0.353 399.8 (ns/day) (hour/ns) Performance: 2.201 10.903 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (378 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes This run will generate roughly 0 Mb of data There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.8%. The balanceable part of the MD step is 40%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 14.452 3.613 400.0 (ns/day) (hour/ns) Performance: 0.215 111.518 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (3634 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.4%. The balanceable part of the MD step is 40%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.8%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.540 0.135 399.4 (ns/day) (hour/ns) Performance: 5.746 4.177 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (159 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.0%. The balanceable part of the MD step is 43%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.3%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.239 0.060 398.6 (ns/day) (hour/ns) Performance: 12.976 1.850 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (81 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 318.937 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.3%. The balanceable part of the MD step is 46%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.5%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.145 0.036 397.6 (ns/day) (hour/ns) Performance: 21.382 1.122 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (59 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.741 0.186 399.5 (ns/day) (hour/ns) Performance: 4.190 5.727 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (207 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.165 0.041 398.0 (ns/day) (hour/ns) Performance: 18.809 1.276 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (63 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.757 0.189 399.5 (ns/day) (hour/ns) Performance: 4.104 5.848 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (210 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.214 0.054 398.4 (ns/day) (hour/ns) Performance: 14.507 1.654 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (75 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.127 0.032 397.3 (ns/day) (hour/ns) Performance: 24.372 0.985 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (54 ms) [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning H bonds into constraints... NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: There are 5 atoms that are fully frozen and part of COMM removal group(s), removing these atoms from the COMM removal group(s) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: There are 3 atoms that are frozen along less then 3 dimensions and part of COMM removal group(s), due to limitations in the code these still contribute to the mass of the COM along frozen dimensions and therefore the COMM correction will be too small. Number of degrees of freedom in T-Coupling group System is 25.50 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 46 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.090 0.023 396.3 (ns/day) (hour/ns) Performance: 34.115 0.703 [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (44 ms) [----------] 12 tests from FreezeWorks/FreezeGroupTest (4971 ms total) [----------] 4 tests from AccelerationWorks/AccelerationGroupTest [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -1207960609 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.2%. The balanceable part of the MD step is 38%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.144 0.036 397.7 (ns/day) (hour/ns) Performance: 42.912 0.559 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (66 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -33594649 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because verlet-buffer-tolerance is not set or used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 37%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 44 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.052 0.013 393.8 (ns/day) (hour/ns) Performance: 117.425 0.204 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (28 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to 2012966796 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.5%. The balanceable part of the MD step is 41%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 43 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.054 0.014 394.1 (ns/day) (hour/ns) Performance: 113.094 0.212 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (29 ms) [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -286487553 Velocities were taken from a Maxwell distribution at 0 K Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 Net Acceleration in X direction, will not be corrected Net Acceleration in Y direction, will not be corrected Net Acceleration in Z direction, will not be corrected This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because verlet-buffer-tolerance is not set or used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 43%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.294 0.074 398.9 (ns/day) (hour/ns) Performance: 21.125 1.136 [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (88 ms) [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (213 ms total) [----------] Global test environment tear-down [==========] 26 tests from 6 test suites ran. (34039 ms total) [ PASSED ] 25 tests. [ SKIPPED ] 1 test, listed below: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 Test time = 34.82 sec ---------------------------------------------------------- Test Passed. "MdrunTestsTwoRanks" end time: Feb 22 23:25 EST "MdrunTestsTwoRanks" time elapsed: 00:00:34 ---------------------------------------------------------- 68/90 Testing: MdrunSingleRankAlgorithmsTests 68/90 Test: MdrunSingleRankAlgorithmsTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-single-rank-algorithms-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunSingleRankAlgorithmsTests" start time: Feb 22 23:25 EST Output: ---------------------------------------------------------- [==========] Running 4 tests from 2 test suites. [----------] Global test environment set-up. [----------] 1 test from OriresTest [ RUN ] OriresTest.OriresCanRun Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 518.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 25, rlist from 1.054 to 1.164 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 10 steps, 0.0 ps. Setting the LD random seed to -604364801 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 8.398 4.199 200.0 (ns/day) (hour/ns) Performance: 0.453 53.023 [ OK ] OriresTest.OriresCanRun (4509 ms) [----------] 1 test from OriresTest (4509 ms total) [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 Number of degrees of freedom in T-Coupling group rest is 10.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Dipoles' 20 steps, 0.1 ps. Setting the LD random seed to 1543491582 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Dipole' Searching the wall atom type(s) The largest distance between excluded atoms is 0.344 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 Estimate for the relative computational load of the PME mesh part: 1.00 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 15.030 7.515 200.0 (ns/day) (hour/ns) Performance: 0.604 39.763 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (8511 ms) [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 Test system 'epsilon-surface-constraint' cannot run with 1 ranks. The supported numbers are > 1. [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: With epsilon_surface > 0 all molecules should be neutral. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: With epsilon_surface > 0 you can only use domain decomposition when there are only small molecules with all bonds constrained (mdrun will check for this). Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Dipoles' 20 steps, 0.1 ps. Setting the LD random seed to 2139614183 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Dipole' The largest distance between excluded atoms is 0.344 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 Estimate for the relative computational load of the PME mesh part: 1.00 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 21.483 10.742 200.0 (ns/day) (hour/ns) Performance: 0.422 56.835 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (11277 ms) [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (19790 ms total) [----------] Global test environment tear-down [==========] 4 tests from 2 test suites ran. (24400 ms total) [ PASSED ] 4 tests. Test time = 25.07 sec ---------------------------------------------------------- Test Passed. "MdrunSingleRankAlgorithmsTests" end time: Feb 22 23:26 EST "MdrunSingleRankAlgorithmsTests" time elapsed: 00:00:25 ---------------------------------------------------------- 69/90 Testing: MdrunNonIntegratorTests 69/90 Test: MdrunNonIntegratorTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-non-integrator-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunNonIntegratorTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunNonIntegratorTests" start time: Feb 22 23:26 EST Output: ---------------------------------------------------------- [==========] Running 58 tests from 5 test suites. [----------] Global test environment set-up. [----------] 1 test from NonbondedBenchTest [ RUN ] NonbondedBenchTest.BasicEndToEndTest SIMD width: 4 System size: 3000 atoms Cut-off radius: 1 nm Number of threads: 1 Number of iterations: 1 Compute energies: no Ewald excl. corr.: analytical Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle total useful Ewald all geom. 4xM 6.724 6.7242 0.1770 0.0937 [ OK ] NonbondedBenchTest.BasicEndToEndTest (11 ms) [----------] 1 test from NonbondedBenchTest (11 ms total) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -4.7991005e+01 Maximum force = 1.8629730e+02 on atom 13 Norm of force = 8.7721930e+01 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (862 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 3.02331e+02 on atom 3 F-Norm = 1.18024e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -5.5862152e+01 Maximum force = 4.2727774e+02 on atom 13 Norm of force = 1.8453139e+02 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (980 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1937741e+02 Maximum force = 9.9988662e+03 on atom 9 Norm of force = 4.6167006e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (932 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 1 NOTE 3 [file glycine_vacuo.top, line 12]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41575e+04 on atom 10 F-Norm = 1.18451e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5174420e+02 Maximum force = 7.4208833e+03 on atom 9 Norm of force = 3.5692977e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1080 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.5698450e+02 Maximum force = 4.5696982e+02 on atom 17 Norm of force = 1.8326277e+02 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1980 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 4 [file unknown]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 1.06801e+03 on atom 28 F-Norm = 4.26918e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.6941083e+02 Maximum force = 2.1829510e+02 on atom 17 Norm of force = 7.9206168e+01 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left This run will generate roughly 0 Mb of data [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2864 ms) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (8702 ms total) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 1 steps Potential Energy = -9.7425687e-01 Maximum force = 4.0132279e+00 on atom 1 Norm of force = 1.6383933e+00 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (157 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 4.01323e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps Potential Energy = -9.9064195e-01 Maximum force = 2.5781672e+00 on atom 1 Norm of force = 1.0525324e+00 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (221 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 4.01323e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps Potential Energy = -9.9064195e-01 Maximum force = 2.5781672e+00 on atom 1 Norm of force = 1.0525324e+00 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (219 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1939679e+02 Maximum force = 9.9704229e+03 on atom 9 Norm of force = 4.6227534e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (735 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5625757e+02 Maximum force = 7.5018237e+03 on atom 9 Norm of force = 3.6139019e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (893 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generating 1-4 interactions: fudge = 1 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022 (single precision) Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to machine precision in 0 steps, but did not reach the requested Fmax < 10. Potential Energy = 5.6111578e+02 Maximum force = 1.2685402e+04 on atom 10 Norm of force = 6.0643536e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' This run will generate roughly 0 Mb of data [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (782 ms) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3009 ms total) [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 12.610 6.305 200.0 (ns/day) (hour/ns) Performance: 0.233 103.023 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Argon', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' trr version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 49 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.944 0.472 199.9 (ns/day) (hour/ns) Performance: 3.110 7.716 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (6921 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 17.312 8.656 200.0 (ns/day) (hour/ns) Performance: 0.170 141.442 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Argon', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 50 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.946 0.473 199.8 (ns/day) (hour/ns) Performance: 3.102 7.736 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (9234 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 15.065 7.535 199.9 (ns/day) (hour/ns) Performance: 0.195 123.125 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Argon', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 51 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.959 0.480 199.8 (ns/day) (hour/ns) Performance: 3.060 7.843 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (8160 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Argon' 16 steps, 0.0 ps. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5.737 2.868 200.0 (ns/day) (hour/ns) Performance: 0.512 46.871 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Argon', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 50 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.962 0.481 199.8 (ns/day) (hour/ns) Performance: 3.051 7.867 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (3496 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 14.885 7.443 200.0 (ns/day) (hour/ns) Performance: 0.197 121.614 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'spc2', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 42 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.829 0.415 199.9 (ns/day) (hour/ns) Performance: 3.543 6.774 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (8133 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 9.623 4.811 200.0 (ns/day) (hour/ns) Performance: 0.305 78.617 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'spc2', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 44 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.835 0.418 199.8 (ns/day) (hour/ns) Performance: 3.515 6.829 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (5451 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 7.400 3.700 200.0 (ns/day) (hour/ns) Performance: 0.397 60.465 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'spc2', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 46 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.085 0.543 199.9 (ns/day) (hour/ns) Performance: 2.706 8.869 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4512 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 16 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 6.434 3.222 199.7 (ns/day) (hour/ns) Performance: 0.456 52.643 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'spc2', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 39 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.940 0.471 199.8 (ns/day) (hour/ns) Performance: 3.121 7.689 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (3970 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 15.285 7.643 200.0 (ns/day) (hour/ns) Performance: 0.192 124.884 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 34 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.370 0.685 199.9 (ns/day) (hour/ns) Performance: 2.144 11.195 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (9026 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 6 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 6 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 32.672 16.336 200.0 (ns/day) (hour/ns) Performance: 0.090 266.931 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 34 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.354 0.682 198.4 (ns/day) (hour/ns) Performance: 2.153 11.146 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (17574 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 12.428 6.214 200.0 (ns/day) (hour/ns) Performance: 0.236 101.544 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 33 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.470 0.735 199.9 (ns/day) (hour/ns) Performance: 1.997 12.015 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (7461 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 22.787 11.394 200.0 (ns/day) (hour/ns) Performance: 0.129 186.172 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 30 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 1.472 0.737 199.9 (ns/day) (hour/ns) Performance: 1.994 12.035 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (12843 ms) [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (96786 ms total) [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun '30 system in water' 16 steps, 0.0 ps. Generated 2485 of the 2485 non-bonded parameter combinations Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Test time = 120.05 sec ---------------------------------------------------------- Test Failed. "MdrunNonIntegratorTests" end time: Feb 22 23:28 EST "MdrunNonIntegratorTests" time elapsed: 00:02:00 ---------------------------------------------------------- 70/90 Testing: MdrunTpiTests 70/90 Test: MdrunTpiTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-tpi-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunTpiTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunTpiTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 2 tests from 1 test suite. [----------] Global test environment set-up. [----------] 2 tests from Simple/TpiTest [ RUN ] Simple/TpiTest.ReproducesOutput/0 Ignoring obsolete mdp entry 'ns_type' Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 1308.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2022 (single precision) TPI is not implemented for GPUs. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Reading frames from gro file '216 water molecules', 648 atoms. Reading frame 0 time 0.000 mu 3.905e+02 3.905e+02 Last frame 0 time 0.000 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Analysing residue names: There are: 216 Water residues There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] Simple/TpiTest.ReproducesOutput/0 (144 ms) [ RUN ] Simple/TpiTest.ReproducesOutput/1 Ignoring obsolete mdp entry 'ns_type' Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 1308.00 Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2022 (single precision) TPI is not implemented for GPUs. Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Reading frames from gro file '216 water molecules', 648 atoms. Reading frame 0 time 0.000 mu 1.070e+02 1.070e+02 Last frame 0 time 0.000 Generated 331705 of the 331705 non-bonded parameter combinations Generated 331705 of the 331705 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 3 bonded neighbours molecule type 'methane' Analysing residue names: There are: 216 Water residues There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] Simple/TpiTest.ReproducesOutput/1 (134 ms) [----------] 2 tests from Simple/TpiTest (278 ms total) [----------] Global test environment tear-down [==========] 2 tests from 1 test suite ran. (323 ms total) [ PASSED ] 2 tests. Test time = 1.03 sec ---------------------------------------------------------- Test Passed. "MdrunTpiTests" end time: Feb 22 23:28 EST "MdrunTpiTests" time elapsed: 00:00:01 ---------------------------------------------------------- 71/90 Testing: MdrunMpiTests 71/90 Test: MdrunMpiTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 17 tests from 4 test suites. [----------] Global test environment set-up. [----------] 1 test from DomainDecompositionSpecialCasesTest [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -304613893 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 9.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc2' 0 steps, 0.0 ps. NOTE: 14 % of the run time was spent in domain decomposition, 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.001 255.0 (ns/day) (hour/ns) Performance: 92.849 0.258 [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (21 ms) [----------] 1 test from DomainDecompositionSpecialCasesTest (21 ms total) [----------] 4 tests from MimicTest [ RUN ] MimicTest.OneQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -405833779 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 340.5 (ns/day) (hour/ns) Performance: 72.674 0.330 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (17 ms) [ RUN ] MimicTest.AllQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 786323933 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 336.4 (ns/day) (hour/ns) Performance: 78.270 0.307 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (15 ms) [ RUN ] MimicTest.TwoQuantumMol NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -16789527 Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/4water.gro' Reading frames from gro file 'Generated by gmx solvate', 12 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 335.0 (ns/day) (hour/ns) Performance: 76.148 0.315 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (17 ms) [ RUN ] MimicTest.BondCuts NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -1111687187 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Number of degrees of freedom in T-Coupling group rest is 66.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: NVE simulation: will use the initial temperature of 300.368 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/ala.gro' Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. Reading frame 0 time 0.000 Last frame 0 time 0.000 Core t (s) Wall t (s) (%) Time: 0.004 0.001 343.4 (ns/day) (hour/ns) Performance: 70.510 0.340 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (23 ms) [----------] 4 tests from MimicTest (74 ms total) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -4.7990936e+01 Maximum force = 1.8629684e+02 on atom 13 Norm of force = 8.7721899e+01 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (17375 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 3.02331e+02 on atom 3 F-Norm = 1.18024e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -5.5862125e+01 Maximum force = 4.2728583e+02 on atom 13 Norm of force = 1.8453393e+02 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (133 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1937720e+02 Maximum force = 9.9988643e+03 on atom 9 Norm of force = 4.6166993e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (63 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... NOTE 3 [file glycine_vacuo.top, line 12]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41575e+04 on atom 10 F-Norm = 1.18451e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5174454e+02 Maximum force = 7.4208896e+03 on atom 9 Norm of force = 3.5693002e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (61 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.5698456e+02 Maximum force = 4.5696985e+02 on atom 17 Norm of force = 1.8326278e+02 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (26 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 4 [file unknown]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 1.06801e+03 on atom 28 F-Norm = 4.26918e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.6941089e+02 Maximum force = 2.1828270e+02 on atom 17 Norm of force = 7.9204032e+01 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (25 ms) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (17686 ms total) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 1 steps Potential Energy = -9.7425687e-01 Maximum force = 4.0132279e+00 on atom 3 Norm of force = 1.6383933e+00 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (18 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 4.01323e+00 on atom 3 F-Norm = 1.63839e+00 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps Potential Energy = -9.9064195e-01 Maximum force = 2.5781672e+00 on atom 3 Norm of force = 1.0525324e+00 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (17 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (9 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.1939664e+02 Maximum force = 9.9704229e+03 on atom 9 Norm of force = 4.6227537e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (62 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022 (single precision) Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.5625764e+02 Maximum force = 7.5018237e+03 on atom 9 Norm of force = 3.6139019e+03 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (62 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (54 ms) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (226 ms total) [----------] Global test environment tear-down [==========] 17 tests from 4 test suites ran. (18248 ms total) [ PASSED ] 17 tests. Test time = 19.03 sec ---------------------------------------------------------- Test Passed. "MdrunMpiTests" end time: Feb 22 23:28 EST "MdrunMpiTests" time elapsed: 00:00:19 ---------------------------------------------------------- 72/90 Testing: MdrunMultiSimTests 72/90 Test: MdrunMultiSimTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "4" "${WORKDIR}/gromacs-2022/build/bin/mdrun-multisim-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMultiSimTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMultiSimTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 6 tests from 2 test suites. [----------] Global test environment set-up. [----------] 4 tests from InNvt/MultiSimTest [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -285379591 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1079854089 Setting the LD random seed to -1074268164 Setting the LD random seed to 1607221111 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -687955975 Velocities were taken from a Maxwell distribution at 278 K Setting gen_seed to -67108902 Setting gen_seed to -1227096386 Velocities were taken from a Maxwell distribution at 298 K Velocities were taken from a Maxwell distribution at 268 K Setting gen_seed to -537937929 Velocities were taken from a Maxwell distribution at 288 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K This run will generate roughly 0 Mb of data There were 2 notes Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm There were 2 notes Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K This run will generate roughly 0 Mb of data There were 2 notes Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (15340 ms) [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1108421256 Setting the LD random seed to -1644269651 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -147046977 Velocities were taken from a Maxwell distribution at 278 K Setting gen_seed to -684466193 Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Number of degrees of freedom in T-Coupling group System is 9.00 This run will generate roughly 0 Mb of data Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K There were 2 notes Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (110 ms) [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 2079768283 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to 2130406242 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -2015384237 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1795295818 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Excluding 2 bonded neighbours molecule type 'SOL' Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generating 1-4 interactions: fudge = 0.5 Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -31473801 Velocities were taken from a Maxwell distribution at 278 K Setting gen_seed to 2129608443 Setting gen_seed to -218227271 Velocities were taken from a Maxwell distribution at 298 K Velocities were taken from a Maxwell distribution at 268 K Setting gen_seed to -373541121 Velocities were taken from a Maxwell distribution at 288 K Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 0 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 3 steps, 0.0 ps. starting mdrun 'spc2' 1 steps, 0.0 ps. Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (16 ms) [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1090654021 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to 1326673491 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -1294212610 Velocities were taken from a Maxwell distribution at 278 K Setting gen_seed to -957425857 Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 1 steps, 0.0 ps. starting mdrun 'spc2' 0 steps, 0.0 ps. Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Note: The number of steps is not consistent across multi simulations, but we are proceeding anyway! Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (16 ms) [----------] 4 tests from InNvt/MultiSimTest (15537 ms total) [----------] 2 tests from InNvt/MultiSimTerminationTest [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -5573891 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to 493877867 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -268444707 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -537018433 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -676481050 Velocities were taken from a Maxwell distribution at 268 K Setting gen_seed to -436233221 Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Setting gen_seed to -16180061 Velocities were taken from a Maxwell distribution at 288 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Setting gen_seed to -1282148433 Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (99 ms) [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -786465 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -675432577 Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -67167265 Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to -34603298 Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 11.9%. The balanceable part of the MD step is 4%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 8.8%. The balanceable part of the MD step is 4%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). starting mdrun 'spc2' 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (160 ms) [----------] 2 tests from InNvt/MultiSimTerminationTest (259 ms total) [----------] Global test environment tear-down [==========] 6 tests from 2 test suites ran. (16204 ms total) [ PASSED ] 6 tests. Test time = 17.28 sec ---------------------------------------------------------- Test Passed. "MdrunMultiSimTests" end time: Feb 22 23:28 EST "MdrunMultiSimTests" time elapsed: 00:00:17 ---------------------------------------------------------- 73/90 Testing: MdrunMultiSimReplexTests 73/90 Test: MdrunMultiSimReplexTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "4" "${WORKDIR}/gromacs-2022/build/bin/mdrun-multisim-replex-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMultiSimReplexTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMultiSimReplexTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 5 tests from 2 test suites. [----------] Global test environment set-up. [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -1689366820 Setting the LD random seed to -788922371 Setting the LD random seed to -553662497 Setting the LD random seed to -9453569 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to 1862163967 Setting gen_seed to 2078277631 Velocities were taken from a Maxwell distribution at 288 K Setting gen_seed to -1166221889 Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to 1471954296 Velocities were taken from a Maxwell distribution at 268 K Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 9.00 Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data This run will generate roughly 0 Mb of data There were 2 notes There were 2 notes NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (121 ms) [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to -543195681 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to -1110582754 Setting the LD random seed to 1916791804 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to -35143877 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to 1223421843 Velocities were taken from a Maxwell distribution at 268 K Setting gen_seed to -33722369 Velocities were taken from a Maxwell distribution at 278 K Setting gen_seed to -1082163361 Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to -577408113 Velocities were taken from a Maxwell distribution at 288 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (46 ms) [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to 1069105023 Setting the LD random seed to -6357057 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -947918946 Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to -342884677 Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.7%. The balanceable part of the MD step is 4%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.0%. The balanceable part of the MD step is 5%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (25 ms) [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to 1819787195 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to -109065475 Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to 933999543 Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to -826413061 Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 2 steps, 0.0 ps. starting mdrun 'spc2' 2 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.7%. The balanceable part of the MD step is 4%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 10.8%. The balanceable part of the MD step is 4%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (69 ms) [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (264 ms total) [----------] 1 test from InNvt/ReplicaExchangeTerminationTest [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -111218529 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -21544998 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -356916225 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Setting the LD random seed to -788543553 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Excluding 2 bonded neighbours molecule type 'SOL' Generating 1-4 interactions: fudge = 0.5 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Setting gen_seed to -285287751 Velocities were taken from a Maxwell distribution at 298 K Setting gen_seed to 1471938559 Velocities were taken from a Maxwell distribution at 268 K Setting gen_seed to -1075843079 Velocities were taken from a Maxwell distribution at 288 K Setting gen_seed to -35672065 Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 9.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. starting mdrun 'spc2' 100 steps, 0.1 ps. Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022 (single precision) Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). starting mdrun 'spc2' 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (103 ms) [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (104 ms total) [----------] Global test environment tear-down [==========] 5 tests from 2 test suites ran. (776 ms total) [ PASSED ] 5 tests. Test time = 1.82 sec ---------------------------------------------------------- Test Passed. "MdrunMultiSimReplexTests" end time: Feb 22 23:28 EST "MdrunMultiSimReplexTests" time elapsed: 00:00:01 ---------------------------------------------------------- 74/90 Testing: MdrunMultiSimReplexEquivalenceTests 74/90 Test: MdrunMultiSimReplexEquivalenceTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "4" "${WORKDIR}/gromacs-2022/build/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMultiSimReplexEquivalenceTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 10 tests from 2 test suites. [----------] Global test environment set-up. [----------] 8 tests from LF/ReplicaExchangeTest [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 268 K Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 288 K Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Number of degrees of freedom in T-Coupling group System is 27.00 Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There were 2 notes Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K This run will generate roughly 0 Mb of data This run will generate roughly 0 Mb of data This run will generate roughly 0 Mb of data There were 2 notes Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (350 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 268 K Velocities were taken from a Maxwell distribution at 288 K Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning Number of degrees of freedom in T-Coupling group System is 27.00 This run will generate roughly 0 Mb of data Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data There was 1 warning Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (325 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 268 K Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Generated 330891 of the 330891 1-4 parameter combinations Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Velocities were taken from a Maxwell distribution at 288 K Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (2738 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 288 K Velocities were taken from a Maxwell distribution at 278 K Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Velocities were taken from a Maxwell distribution at 268 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (446 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 278 K Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.0%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 6.1%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.1%. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (3286 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Velocities were taken from a Maxwell distribution at 278 K Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.2%. The balanceable part of the MD step is 14%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.6%. The balanceable part of the MD step is 14%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (194 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.7%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.1%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (172 ms) [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 278 K Velocities were taken from a Maxwell distribution at 298 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.3%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.1%. The balanceable part of the MD step is 18%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (249 ms) [----------] 8 tests from LF/ReplicaExchangeTest (7767 ms total) [----------] 2 tests from VV/ReplicaExchangeTest [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Generated 330891 of the 330891 1-4 parameter combinations Velocities were taken from a Maxwell distribution at 288 K Generated 330891 of the 330891 1-4 parameter combinations Velocities were taken from a Maxwell distribution at 268 K Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes This run will generate roughly 0 Mb of data Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread Using 1 OpenMP thread Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Writing final coordinates. Writing final coordinates. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (2352 ms) [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Velocities were taken from a Maxwell distribution at 298 K Velocities were taken from a Maxwell distribution at 278 K Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 This is simulation 0 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes This is simulation 1 out of 2 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.3%. The balanceable part of the MD step is 15%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.0%. The balanceable part of the MD step is 15%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (209 ms) [----------] 2 tests from VV/ReplicaExchangeTest (2562 ms total) [----------] Global test environment tear-down [==========] 10 tests from 2 test suites ran. (10741 ms total) [ PASSED ] 10 tests. Test time = 11.77 sec ---------------------------------------------------------- Test Passed. "MdrunMultiSimReplexEquivalenceTests" end time: Feb 22 23:28 EST "MdrunMultiSimReplexEquivalenceTests" time elapsed: 00:00:11 ---------------------------------------------------------- 75/90 Testing: MdrunMpi1RankPmeTests 75/90 Test: MdrunMpi1RankPmeTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "1" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpi1RankPmeTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpi1RankPmeTests" start time: Feb 22 23:28 EST Output: ---------------------------------------------------------- [==========] Running 19 tests from 1 test suite. [----------] Global test environment set-up. [----------] 19 tests from ReproducesEnergies/PmeTest Setting the LD random seed to -1828913969 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 12.00 The largest distance between excluded atoms is 0.190 nm NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 2 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -104103969 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Searching the wall atom type(s) Number of degrees of freedom in T-Coupling group rest is 13.00 The largest distance between excluded atoms is 0.190 nm NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: NVE simulation: will use the initial temperature of 966.268 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 3 notes [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.107 2.054 200.0 (ns/day) (hour/ns) Performance: 0.884 27.164 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (2244 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.134 0.067 199.7 (ns/day) (hour/ns) Performance: 27.132 0.885 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (76 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 0 steps, 0.0 ps. Core t (s) Wall t (s) (%) Time: 0.006 0.003 190.7 (ns/day) (hour/ns) Performance: 26.846 0.894 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (622 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets using PME rank(s) but the simulation is using only one rank it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.289 1.144 200.0 (ns/day) (hour/ns) Performance: 1.585 15.139 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (1155 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (1 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu ${WORKDIR}/gromacs-2022/src/programs/mdrun/tests/pmetest.cpp:316: Skipped Test is being skipped because: it targets GPU execution, but no compatible devices were detected PME GPU does not support: Non-GPU build of GROMACS. [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [----------] 19 tests from ReproducesEnergies/PmeTest (4112 ms total) [----------] Global test environment tear-down [==========] 19 tests from 1 test suite ran. (4174 ms total) [ PASSED ] 4 tests. [ SKIPPED ] 15 tests, listed below: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu Test time = 4.87 sec ---------------------------------------------------------- Test Passed. "MdrunMpi1RankPmeTests" end time: Feb 22 23:29 EST "MdrunMpi1RankPmeTests" time elapsed: 00:00:04 ---------------------------------------------------------- 76/90 Testing: MdrunMpi2RankPmeTests 76/90 Test: MdrunMpi2RankPmeTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpi2RankPmeTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpi2RankPmeTests" start time: Feb 22 23:29 EST Output: ---------------------------------------------------------- [==========] Running 19 tests from 1 test suite. [----------] Global test environment set-up. [----------] 19 tests from ReproducesEnergies/PmeTest Setting the LD random seed to -541902030 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group rest is 12.00 The largest distance between excluded atoms is 0.190 nm NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: NVE simulation: will use the initial temperature of 1046.791 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. This run will generate roughly 0 Mb of data There were 2 notes NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Setting the LD random seed to -268984333 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' Excluding 2 bonded neighbours molecule type 'SOL' Searching the wall atom type(s) Number of degrees of freedom in T-Coupling group rest is 13.00 The largest distance between excluded atoms is 0.190 nm NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: NVE simulation: will use the initial temperature of 966.268 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 Estimate for the relative computational load of the PME mesh part: 1.00 This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. There were 3 notes [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 6.7%. The balanceable part of the MD step is 20%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.4%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 7.766 1.942 399.9 (ns/day) (hour/ns) Performance: 0.934 25.684 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (2130 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 6.8%. The balanceable part of the MD step is 21%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.4%. NOTE: 35 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.127 0.032 398.3 (ns/day) (hour/ns) Performance: 56.679 0.423 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (42 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 0 steps, 0.0 ps. Core t (s) Wall t (s) (%) Time: 0.007 0.002 335.5 (ns/day) (hour/ns) Performance: 42.744 0.561 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (604 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 32.923 8.231 400.0 (ns/day) (hour/ns) Performance: 0.220 108.875 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (8291 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.252 0.313 399.9 (ns/day) (hour/ns) Performance: 5.793 4.143 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (321 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (1 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 0 steps, 0.0 ps. Core t (s) Wall t (s) (%) Time: 0.880 0.220 399.7 (ns/day) (hour/ns) Performance: 0.392 61.184 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (445 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads per MPI process starting mdrun 'spc-and-methanol' 20 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 6.4%. The balanceable part of the MD step is 21%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.3%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 78.619 19.655 400.0 (ns/day) (hour/ns) Performance: 0.092 259.987 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (19666 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) [----------] 19 tests from ReproducesEnergies/PmeTest (31515 ms total) [----------] Global test environment tear-down [==========] 19 tests from 1 test suite ran. (31590 ms total) [ PASSED ] 7 tests. [ SKIPPED ] 12 tests, listed below: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu Test time = 32.42 sec ---------------------------------------------------------- Test Passed. "MdrunMpi2RankPmeTests" end time: Feb 22 23:29 EST "MdrunMpi2RankPmeTests" time elapsed: 00:00:32 ---------------------------------------------------------- 77/90 Testing: MdrunMpiCoordinationBasicTestsOneRank 77/90 Test: MdrunMpiCoordinationBasicTestsOneRank Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "1" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-basic-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationBasicTestsOneRank.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationBasicTestsOneRank" start time: Feb 22 23:29 EST Output: ---------------------------------------------------------- [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from BasicPropagators/PeriodicActionsTest [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.757 0.758 100.0 (ns/day) (hour/ns) Performance: 1.939 12.378 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.279 0.279 100.0 (ns/day) (hour/ns) Performance: 5.262 4.561 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.417 1.417 100.0 (ns/day) (hour/ns) Performance: 1.036 23.158 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.104 0.105 99.7 (ns/day) (hour/ns) Performance: 14.024 1.711 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.045 0.046 99.4 (ns/day) (hour/ns) Performance: 32.110 0.747 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.067 0.067 99.7 (ns/day) (hour/ns) Performance: 21.843 1.099 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2768 ms) [----------] 1 test from BasicPropagators/PeriodicActionsTest (2768 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (2810 ms total) [ PASSED ] 1 test. Test time = 3.50 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationBasicTestsOneRank" end time: Feb 22 23:29 EST "MdrunMpiCoordinationBasicTestsOneRank" time elapsed: 00:00:03 ---------------------------------------------------------- 78/90 Testing: MdrunMpiCoordinationBasicTestsTwoRanks 78/90 Test: MdrunMpiCoordinationBasicTestsTwoRanks Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-basic-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationBasicTestsTwoRanks.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationBasicTestsTwoRanks" start time: Feb 22 23:29 EST Output: ---------------------------------------------------------- [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from BasicPropagators/PeriodicActionsTest [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 22%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 3.009 1.505 199.9 (ns/day) (hour/ns) Performance: 0.976 24.588 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K There were 3 notes Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 28%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.050 0.025 199.0 (ns/day) (hour/ns) Performance: 58.350 0.411 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Last energy frame read 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.2%. The balanceable part of the MD step is 48%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 198.3 (ns/day) (hour/ns) Performance: 104.356 0.230 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.030 0.015 197.2 (ns/day) (hour/ns) Performance: 98.049 0.245 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.4%. The balanceable part of the MD step is 33%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.052 0.026 198.4 (ns/day) (hour/ns) Performance: 56.041 0.428 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (1). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 196.7 (ns/day) (hour/ns) Performance: 110.585 0.217 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1682 ms) [----------] 1 test from BasicPropagators/PeriodicActionsTest (1682 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (1745 ms total) [ PASSED ] 1 test. Test time = 2.53 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationBasicTestsTwoRanks" end time: Feb 22 23:29 EST "MdrunMpiCoordinationBasicTestsTwoRanks" time elapsed: 00:00:02 ---------------------------------------------------------- 79/90 Testing: MdrunMpiCoordinationCouplingTestsOneRank 79/90 Test: MdrunMpiCoordinationCouplingTestsOneRank Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "1" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-coupling-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationCouplingTestsOneRank.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationCouplingTestsOneRank" start time: Feb 22 23:29 EST Output: ---------------------------------------------------------- [==========] Running 25 tests from 1 test suite. [----------] Global test environment set-up. [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5.040 5.040 100.0 (ns/day) (hour/ns) Performance: 0.291 82.350 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 22.677 22.677 100.0 (ns/day) (hour/ns) Performance: 0.065 370.544 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.603 0.604 100.0 (ns/day) (hour/ns) Performance: 2.434 9.861 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.4 (ns/day) (hour/ns) Performance: 119.371 0.201 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.014 98.6 (ns/day) (hour/ns) Performance: 104.858 0.229 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.8 (ns/day) (hour/ns) Performance: 99.726 0.241 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (28449 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.079 0.080 99.8 (ns/day) (hour/ns) Performance: 18.471 1.299 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.028 99.6 (ns/day) (hour/ns) Performance: 53.164 0.451 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.3 (ns/day) (hour/ns) Performance: 84.459 0.284 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.015 98.7 (ns/day) (hour/ns) Performance: 100.797 0.238 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.037 0.038 99.5 (ns/day) (hour/ns) Performance: 39.131 0.613 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.017 98.8 (ns/day) (hour/ns) Performance: 88.718 0.271 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (269 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.029 99.3 (ns/day) (hour/ns) Performance: 50.892 0.472 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.014 99.2 (ns/day) (hour/ns) Performance: 105.241 0.228 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 99.1 (ns/day) (hour/ns) Performance: 115.190 0.208 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.7 (ns/day) (hour/ns) Performance: 98.647 0.243 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.7 (ns/day) (hour/ns) Performance: 96.171 0.250 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.5 (ns/day) (hour/ns) Performance: 118.198 0.203 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (175 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.029 99.3 (ns/day) (hour/ns) Performance: 51.361 0.467 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.022 99.5 (ns/day) (hour/ns) Performance: 66.855 0.359 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 99.1 (ns/day) (hour/ns) Performance: 121.048 0.198 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.010 98.2 (ns/day) (hour/ns) Performance: 142.616 0.168 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.010 98.2 (ns/day) (hour/ns) Performance: 143.963 0.167 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.8 (ns/day) (hour/ns) Performance: 97.546 0.246 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (170 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.056 0.056 99.6 (ns/day) (hour/ns) Performance: 26.168 0.917 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.035 0.035 99.7 (ns/day) (hour/ns) Performance: 41.798 0.574 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.012 99.0 (ns/day) (hour/ns) Performance: 127.591 0.188 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 98.3 (ns/day) (hour/ns) Performance: 130.493 0.184 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.3 (ns/day) (hour/ns) Performance: 117.674 0.204 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.012 98.1 (ns/day) (hour/ns) Performance: 126.459 0.190 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (216 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.287 0.287 99.9 (ns/day) (hour/ns) Performance: 5.113 4.694 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.4 (ns/day) (hour/ns) Performance: 76.043 0.316 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.010 98.8 (ns/day) (hour/ns) Performance: 150.346 0.160 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.075 0.075 99.7 (ns/day) (hour/ns) Performance: 19.657 1.221 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.080 0.080 99.7 (ns/day) (hour/ns) Performance: 18.416 1.303 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.018 98.9 (ns/day) (hour/ns) Performance: 83.605 0.287 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (565 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.032 99.4 (ns/day) (hour/ns) Performance: 46.127 0.520 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.4 (ns/day) (hour/ns) Performance: 75.368 0.318 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 99.1 (ns/day) (hour/ns) Performance: 120.682 0.199 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.039 0.039 99.5 (ns/day) (hour/ns) Performance: 37.800 0.635 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.4 (ns/day) (hour/ns) Performance: 124.537 0.193 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.013 98.5 (ns/day) (hour/ns) Performance: 117.024 0.205 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (199 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.030 99.3 (ns/day) (hour/ns) Performance: 49.603 0.484 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.011 99.0 (ns/day) (hour/ns) Performance: 139.339 0.172 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 99.0 (ns/day) (hour/ns) Performance: 135.457 0.177 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.194 0.194 99.9 (ns/day) (hour/ns) Performance: 7.577 3.167 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.023 99.2 (ns/day) (hour/ns) Performance: 64.131 0.374 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 98.6 (ns/day) (hour/ns) Performance: 111.737 0.215 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (353 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.108 0.108 99.8 (ns/day) (hour/ns) Performance: 13.583 1.767 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.3 (ns/day) (hour/ns) Performance: 90.736 0.265 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.009 0.009 98.8 (ns/day) (hour/ns) Performance: 157.637 0.152 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.014 98.5 (ns/day) (hour/ns) Performance: 107.530 0.223 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.057 0.057 99.7 (ns/day) (hour/ns) Performance: 25.636 0.936 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.4 (ns/day) (hour/ns) Performance: 119.519 0.201 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (290 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.040 0.040 99.5 (ns/day) (hour/ns) Performance: 36.385 0.660 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.053 0.054 99.8 (ns/day) (hour/ns) Performance: 27.450 0.874 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 99.2 (ns/day) (hour/ns) Performance: 110.520 0.217 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.0 (ns/day) (hour/ns) Performance: 81.454 0.295 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.015 98.7 (ns/day) (hour/ns) Performance: 101.023 0.238 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.051 0.051 99.6 (ns/day) (hour/ns) Performance: 28.771 0.834 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (275 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.052 0.052 99.6 (ns/day) (hour/ns) Performance: 28.070 0.855 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.4 (ns/day) (hour/ns) Performance: 84.699 0.283 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.3 (ns/day) (hour/ns) Performance: 93.356 0.257 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 98.4 (ns/day) (hour/ns) Performance: 124.663 0.193 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.7 (ns/day) (hour/ns) Performance: 97.057 0.247 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.011 98.2 (ns/day) (hour/ns) Performance: 138.210 0.174 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (195 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.300 0.300 99.9 (ns/day) (hour/ns) Performance: 4.897 4.900 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.040 0.040 99.7 (ns/day) (hour/ns) Performance: 36.748 0.653 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.009 0.009 98.8 (ns/day) (hour/ns) Performance: 161.137 0.149 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.082 0.082 99.8 (ns/day) (hour/ns) Performance: 17.812 1.347 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.024 99.2 (ns/day) (hour/ns) Performance: 62.065 0.387 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.089 0.089 99.8 (ns/day) (hour/ns) Performance: 16.551 1.450 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (619 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.094 0.094 99.7 (ns/day) (hour/ns) Performance: 15.657 1.533 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.033 99.7 (ns/day) (hour/ns) Performance: 44.613 0.538 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.084 0.084 99.9 (ns/day) (hour/ns) Performance: 17.388 1.380 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.0 (ns/day) (hour/ns) Performance: 76.219 0.315 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 98.3 (ns/day) (hour/ns) Performance: 135.974 0.177 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 98.9 (ns/day) (hour/ns) Performance: 87.947 0.273 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (335 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.050 0.051 99.6 (ns/day) (hour/ns) Performance: 28.994 0.828 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.030 99.6 (ns/day) (hour/ns) Performance: 49.278 0.487 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.020 99.5 (ns/day) (hour/ns) Performance: 75.226 0.319 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.010 0.010 98.2 (ns/day) (hour/ns) Performance: 143.170 0.168 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.7 (ns/day) (hour/ns) Performance: 99.530 0.241 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 98.6 (ns/day) (hour/ns) Performance: 110.152 0.218 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (211 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.081 0.081 99.8 (ns/day) (hour/ns) Performance: 18.059 1.329 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.023 99.5 (ns/day) (hour/ns) Performance: 63.138 0.380 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.4 (ns/day) (hour/ns) Performance: 80.753 0.297 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.027 0.027 99.2 (ns/day) (hour/ns) Performance: 53.523 0.448 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.030 99.3 (ns/day) (hour/ns) Performance: 49.398 0.486 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 98.8 (ns/day) (hour/ns) Performance: 95.244 0.252 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (277 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.056 0.056 99.7 (ns/day) (hour/ns) Performance: 26.085 0.920 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.032 99.7 (ns/day) (hour/ns) Performance: 46.375 0.518 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 99.1 (ns/day) (hour/ns) Performance: 122.772 0.195 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 98.8 (ns/day) (hour/ns) Performance: 92.023 0.261 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 98.4 (ns/day) (hour/ns) Performance: 114.928 0.209 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 98.6 (ns/day) (hour/ns) Performance: 108.881 0.220 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (217 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.037 0.037 99.9 (ns/day) (hour/ns) Performance: 39.443 0.608 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.072 0.072 100.0 (ns/day) (hour/ns) Performance: 20.326 1.181 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.021 100.0 (ns/day) (hour/ns) Performance: 69.753 0.344 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.9 (ns/day) (hour/ns) Performance: 81.705 0.294 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.014 99.9 (ns/day) (hour/ns) Performance: 105.858 0.227 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.068 0.068 100.0 (ns/day) (hour/ns) Performance: 21.502 1.116 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (310 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.048 0.048 100.0 (ns/day) (hour/ns) Performance: 30.882 0.777 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.205 0.205 100.0 (ns/day) (hour/ns) Performance: 7.153 3.355 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.079 0.079 100.0 (ns/day) (hour/ns) Performance: 18.648 1.287 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.029 100.0 (ns/day) (hour/ns) Performance: 49.922 0.481 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.9 (ns/day) (hour/ns) Performance: 84.678 0.283 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 99.9 (ns/day) (hour/ns) Performance: 99.004 0.242 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (466 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.039 0.039 100.0 (ns/day) (hour/ns) Performance: 37.397 0.642 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.9 (ns/day) (hour/ns) Performance: 88.147 0.272 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.012 0.012 99.9 (ns/day) (hour/ns) Performance: 117.506 0.204 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.022 100.0 (ns/day) (hour/ns) Performance: 65.813 0.365 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.022 99.9 (ns/day) (hour/ns) Performance: 68.179 0.352 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.9 (ns/day) (hour/ns) Performance: 93.643 0.256 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (204 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.155 0.155 100.0 (ns/day) (hour/ns) Performance: 9.446 2.541 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.031 0.031 99.9 (ns/day) (hour/ns) Performance: 46.637 0.515 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 99.9 (ns/day) (hour/ns) Performance: 114.975 0.209 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.067 0.067 100.0 (ns/day) (hour/ns) Performance: 22.025 1.090 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 99.9 (ns/day) (hour/ns) Performance: 134.247 0.179 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.009 0.009 99.9 (ns/day) (hour/ns) Performance: 161.053 0.149 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (365 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.118 0.118 100.0 (ns/day) (hour/ns) Performance: 12.461 1.926 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.058 0.058 100.0 (ns/day) (hour/ns) Performance: 25.153 0.954 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 99.9 (ns/day) (hour/ns) Performance: 134.376 0.179 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 99.9 (ns/day) (hour/ns) Performance: 98.436 0.244 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 99.9 (ns/day) (hour/ns) Performance: 112.072 0.214 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.013 0.013 99.9 (ns/day) (hour/ns) Performance: 116.227 0.206 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (301 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.9 (ns/day) (hour/ns) Performance: 81.520 0.294 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 99.9 (ns/day) (hour/ns) Performance: 132.743 0.181 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.008 0.008 99.8 (ns/day) (hour/ns) Performance: 173.041 0.139 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 99.9 (ns/day) (hour/ns) Performance: 98.398 0.244 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.021 99.9 (ns/day) (hour/ns) Performance: 69.173 0.347 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 99.9 (ns/day) (hour/ns) Performance: 100.065 0.240 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (162 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.036 0.036 100.0 (ns/day) (hour/ns) Performance: 40.472 0.593 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.022 99.9 (ns/day) (hour/ns) Performance: 65.853 0.364 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.011 0.011 99.9 (ns/day) (hour/ns) Performance: 127.842 0.188 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.241 0.241 100.0 (ns/day) (hour/ns) Performance: 6.085 3.944 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.355 1.355 100.0 (ns/day) (hour/ns) Performance: 1.084 22.139 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.085 0.085 100.0 (ns/day) (hour/ns) Performance: 17.201 1.395 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1832 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.040 0.040 99.9 (ns/day) (hour/ns) Performance: 36.352 0.660 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.025 0.025 99.9 (ns/day) (hour/ns) Performance: 58.125 0.413 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.9 (ns/day) (hour/ns) Performance: 84.796 0.283 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.056 0.056 100.0 (ns/day) (hour/ns) Performance: 26.218 0.915 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.067 0.067 100.0 (ns/day) (hour/ns) Performance: 21.853 1.098 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.9 (ns/day) (hour/ns) Performance: 78.286 0.307 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (297 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.062 0.062 100.0 (ns/day) (hour/ns) Performance: 23.776 1.009 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.028 100.0 (ns/day) (hour/ns) Performance: 51.798 0.463 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.015 0.015 99.9 (ns/day) (hour/ns) Performance: 100.306 0.239 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.9 (ns/day) (hour/ns) Performance: 89.054 0.269 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.021 99.9 (ns/day) (hour/ns) Performance: 71.562 0.335 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.9 (ns/day) (hour/ns) Performance: 92.812 0.259 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (229 ms) [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (36993 ms total) [----------] Global test environment tear-down [==========] 25 tests from 1 test suite ran. (37035 ms total) [ PASSED ] 25 tests. Test time = 37.72 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationCouplingTestsOneRank" end time: Feb 22 23:30 EST "MdrunMpiCoordinationCouplingTestsOneRank" time elapsed: 00:00:37 ---------------------------------------------------------- 80/90 Testing: MdrunMpiCoordinationCouplingTestsTwoRanks 80/90 Test: MdrunMpiCoordinationCouplingTestsTwoRanks Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-coupling-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationCouplingTestsTwoRanks.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationCouplingTestsTwoRanks" start time: Feb 22 23:30 EST Output: ---------------------------------------------------------- [==========] Running 25 tests from 1 test suite. [----------] Global test environment set-up. [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.0%. The balanceable part of the MD step is 23%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.817 0.909 199.9 (ns/day) (hour/ns) Performance: 1.616 14.853 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 24%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.071 0.035 199.3 (ns/day) (hour/ns) Performance: 41.458 0.579 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.2%. The balanceable part of the MD step is 46%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.032 0.016 198.5 (ns/day) (hour/ns) Performance: 90.950 0.264 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.5%. The balanceable part of the MD step is 22%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.175 0.088 199.5 (ns/day) (hour/ns) Performance: 16.703 1.437 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 29%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.035 0.018 197.8 (ns/day) (hour/ns) Performance: 82.492 0.291 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.3%. The balanceable part of the MD step is 29%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 197.0 (ns/day) (hour/ns) Performance: 111.882 0.215 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1165 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 19%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.802 0.401 199.9 (ns/day) (hour/ns) Performance: 3.662 6.553 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.7%. The balanceable part of the MD step is 25%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 2.613 1.307 200.0 (ns/day) (hour/ns) Performance: 1.124 21.351 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.2%. The balanceable part of the MD step is 48%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.163 0.081 199.7 (ns/day) (hour/ns) Performance: 18.042 1.330 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.6%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.073 0.037 198.9 (ns/day) (hour/ns) Performance: 40.059 0.599 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.6%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.027 0.014 197.1 (ns/day) (hour/ns) Performance: 108.109 0.222 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.4%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 196.9 (ns/day) (hour/ns) Performance: 111.642 0.215 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1931 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.0%. The balanceable part of the MD step is 22%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.740 0.370 199.9 (ns/day) (hour/ns) Performance: 3.965 6.053 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.3%. The balanceable part of the MD step is 28%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 4.794 2.397 200.0 (ns/day) (hour/ns) Performance: 0.613 39.171 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.001 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.1%. The balanceable part of the MD step is 50%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.1%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.259 0.130 199.8 (ns/day) (hour/ns) Performance: 11.334 2.118 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.069 0.035 198.8 (ns/day) (hour/ns) Performance: 42.403 0.566 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.6%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.074 0.037 198.9 (ns/day) (hour/ns) Performance: 39.572 0.606 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.0%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.104 0.052 199.2 (ns/day) (hour/ns) Performance: 28.148 0.853 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3101 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 19%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.501 0.251 199.8 (ns/day) (hour/ns) Performance: 5.862 4.094 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.2%. The balanceable part of the MD step is 25%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.128 0.064 199.6 (ns/day) (hour/ns) Performance: 22.896 1.048 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.4%. The balanceable part of the MD step is 48%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.2%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.025 0.013 198.0 (ns/day) (hour/ns) Performance: 116.189 0.207 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.7%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.060 0.030 198.7 (ns/day) (hour/ns) Performance: 48.517 0.495 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.5%. The balanceable part of the MD step is 32%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.052 0.026 198.4 (ns/day) (hour/ns) Performance: 56.139 0.428 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.4%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.042 0.021 197.6 (ns/day) (hour/ns) Performance: 69.610 0.345 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (481 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.076 0.038 198.8 (ns/day) (hour/ns) Performance: 38.525 0.623 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.031 0.016 198.5 (ns/day) (hour/ns) Performance: 93.065 0.258 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 197.9 (ns/day) (hour/ns) Performance: 124.178 0.193 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 197.1 (ns/day) (hour/ns) Performance: 103.479 0.232 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 197.2 (ns/day) (hour/ns) Performance: 102.312 0.235 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.024 0.012 196.6 (ns/day) (hour/ns) Performance: 121.346 0.198 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (182 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.058 0.029 198.5 (ns/day) (hour/ns) Performance: 50.312 0.477 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.152 0.076 199.7 (ns/day) (hour/ns) Performance: 19.317 1.242 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 14 time 0.014 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Last energy frame read 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.021 0.011 197.7 (ns/day) (hour/ns) Performance: 138.999 0.173 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.021 0.011 196.2 (ns/day) (hour/ns) Performance: 135.221 0.177 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup There were 2 notes There was 1 warning This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.021 0.011 196.3 (ns/day) (hour/ns) Performance: 134.232 0.179 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 196.8 (ns/day) (hour/ns) Performance: 111.381 0.215 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (228 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.091 0.046 199.1 (ns/day) (hour/ns) Performance: 32.075 0.748 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.039 0.020 198.7 (ns/day) (hour/ns) Performance: 75.228 0.319 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.027 0.013 198.1 (ns/day) (hour/ns) Performance: 109.210 0.220 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.031 0.016 197.4 (ns/day) (hour/ns) Performance: 94.089 0.255 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.027 0.014 197.1 (ns/day) (hour/ns) Performance: 106.160 0.226 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.022 0.011 196.6 (ns/day) (hour/ns) Performance: 129.003 0.186 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (194 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.049 0.025 198.3 (ns/day) (hour/ns) Performance: 59.849 0.401 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.070 0.035 199.3 (ns/day) (hour/ns) Performance: 41.799 0.574 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.016 0.008 197.0 (ns/day) (hour/ns) Performance: 178.936 0.134 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 196.3 (ns/day) (hour/ns) Performance: 126.410 0.190 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.040 0.020 198.0 (ns/day) (hour/ns) Performance: 73.438 0.327 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 197.2 (ns/day) (hour/ns) Performance: 102.679 0.234 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (189 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.045 0.023 198.1 (ns/day) (hour/ns) Performance: 64.599 0.372 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.034 0.017 198.6 (ns/day) (hour/ns) Performance: 86.776 0.277 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.037 0.019 198.7 (ns/day) (hour/ns) Performance: 78.938 0.304 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.025 0.013 196.9 (ns/day) (hour/ns) Performance: 116.875 0.205 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 196.9 (ns/day) (hour/ns) Performance: 112.356 0.214 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 197.2 (ns/day) (hour/ns) Performance: 102.575 0.234 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (173 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.259 0.130 199.7 (ns/day) (hour/ns) Performance: 11.320 2.120 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.083 0.042 199.4 (ns/day) (hour/ns) Performance: 35.343 0.679 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.202 0.101 199.7 (ns/day) (hour/ns) Performance: 14.523 1.653 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.472 0.236 199.8 (ns/day) (hour/ns) Performance: 6.217 3.860 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.213 0.607 199.9 (ns/day) (hour/ns) Performance: 2.421 9.913 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.079 0.040 199.0 (ns/day) (hour/ns) Performance: 36.978 0.649 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1235 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.089 0.044 199.0 (ns/day) (hour/ns) Performance: 33.007 0.727 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.164 0.082 199.7 (ns/day) (hour/ns) Performance: 17.857 1.344 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 198.1 (ns/day) (hour/ns) Performance: 113.601 0.211 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.029 0.015 197.2 (ns/day) (hour/ns) Performance: 100.649 0.238 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.032 0.016 197.5 (ns/day) (hour/ns) Performance: 91.653 0.262 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 196.5 (ns/day) (hour/ns) Performance: 124.083 0.193 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (263 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.056 0.028 198.5 (ns/day) (hour/ns) Performance: 51.789 0.463 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.062 0.031 199.2 (ns/day) (hour/ns) Performance: 47.116 0.509 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.017 0.009 197.1 (ns/day) (hour/ns) Performance: 171.540 0.140 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.051 0.026 198.4 (ns/day) (hour/ns) Performance: 56.693 0.423 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 196.5 (ns/day) (hour/ns) Performance: 127.148 0.189 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.087 0.044 199.1 (ns/day) (hour/ns) Performance: 33.505 0.716 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (227 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.071 0.036 198.9 (ns/day) (hour/ns) Performance: 41.178 0.583 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.090 0.045 199.5 (ns/day) (hour/ns) Performance: 32.655 0.735 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Last energy frame read 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.030 0.015 198.4 (ns/day) (hour/ns) Performance: 96.980 0.247 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.038 0.019 198.0 (ns/day) (hour/ns) Performance: 75.944 0.316 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.032 0.016 197.6 (ns/day) (hour/ns) Performance: 90.918 0.264 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.075 0.038 199.0 (ns/day) (hour/ns) Performance: 38.813 0.618 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (244 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.097 0.049 199.1 (ns/day) (hour/ns) Performance: 30.227 0.794 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.020 0.010 197.7 (ns/day) (hour/ns) Performance: 141.936 0.169 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.015 0.008 196.8 (ns/day) (hour/ns) Performance: 195.814 0.123 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.017 0.009 195.4 (ns/day) (hour/ns) Performance: 166.258 0.144 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.021 0.010 196.2 (ns/day) (hour/ns) Performance: 140.505 0.171 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.118 0.059 199.4 (ns/day) (hour/ns) Performance: 24.852 0.966 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (219 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.291 0.146 199.7 (ns/day) (hour/ns) Performance: 10.069 2.384 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.037 0.018 198.7 (ns/day) (hour/ns) Performance: 79.809 0.301 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.021 0.010 197.7 (ns/day) (hour/ns) Performance: 140.820 0.170 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.029 0.015 197.3 (ns/day) (hour/ns) Performance: 99.429 0.241 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.018 0.009 195.7 (ns/day) (hour/ns) Performance: 161.916 0.148 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.060 0.030 198.6 (ns/day) (hour/ns) Performance: 48.353 0.496 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (314 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.074 0.037 198.9 (ns/day) (hour/ns) Performance: 39.487 0.608 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.124 0.062 199.6 (ns/day) (hour/ns) Performance: 23.597 1.017 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 198.0 (ns/day) (hour/ns) Performance: 126.309 0.190 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.059 0.030 198.7 (ns/day) (hour/ns) Performance: 49.730 0.483 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.020 0.010 196.1 (ns/day) (hour/ns) Performance: 140.616 0.171 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 196.7 (ns/day) (hour/ns) Performance: 126.624 0.190 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (238 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.7%. The balanceable part of the MD step is 21%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.150 0.076 198.5 (ns/day) (hour/ns) Performance: 19.404 1.237 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.2%. The balanceable part of the MD step is 29%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.070 0.036 198.0 (ns/day) (hour/ns) Performance: 41.351 0.580 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.5%. The balanceable part of the MD step is 54%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.147 0.074 199.0 (ns/day) (hour/ns) Performance: 19.909 1.206 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 4.5%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.5%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.048 0.024 196.6 (ns/day) (hour/ns) Performance: 60.017 0.400 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.2%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.460 0.231 199.6 (ns/day) (hour/ns) Performance: 6.367 3.769 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.068 0.035 197.5 (ns/day) (hour/ns) Performance: 42.558 0.564 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (555 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.7%. The balanceable part of the MD step is 21%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.186 0.093 198.8 (ns/day) (hour/ns) Performance: 15.716 1.527 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.5%. The balanceable part of the MD step is 28%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.091 0.046 198.4 (ns/day) (hour/ns) Performance: 32.019 0.750 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 56%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 4.657 2.330 199.9 (ns/day) (hour/ns) Performance: 0.630 38.067 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.5%. The balanceable part of the MD step is 38%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.111 0.556 199.8 (ns/day) (hour/ns) Performance: 2.643 9.080 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 38%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.073 0.037 197.8 (ns/day) (hour/ns) Performance: 39.632 0.606 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 37%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.096 0.049 198.3 (ns/day) (hour/ns) Performance: 30.242 0.794 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3197 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.7%. The balanceable part of the MD step is 22%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.066 0.033 196.8 (ns/day) (hour/ns) Performance: 43.860 0.547 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.3%. The balanceable part of the MD step is 26%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. NOTE: 47 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.038 0.019 196.1 (ns/day) (hour/ns) Performance: 76.283 0.315 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.2%. The balanceable part of the MD step is 57%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.7%. NOTE: 46 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.022 0.012 193.8 (ns/day) (hour/ns) Performance: 126.736 0.189 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 3.9%. The balanceable part of the MD step is 39%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.5%. NOTE: 46 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 194.2 (ns/day) (hour/ns) Performance: 102.770 0.234 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 38%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 46 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.029 0.015 194.3 (ns/day) (hour/ns) Performance: 99.662 0.241 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.9%. The balanceable part of the MD step is 38%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.1%. NOTE: 45 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.027 0.014 194.0 (ns/day) (hour/ns) Performance: 106.314 0.226 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (186 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.083 0.042 197.3 (ns/day) (hour/ns) Performance: 35.128 0.683 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.107 0.054 198.6 (ns/day) (hour/ns) Performance: 27.317 0.879 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.137 0.069 198.9 (ns/day) (hour/ns) Performance: 21.375 1.123 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 1 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.015 194.6 (ns/day) (hour/ns) Performance: 96.108 0.250 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.026 0.014 193.9 (ns/day) (hour/ns) Performance: 108.797 0.221 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.044 0.022 196.3 (ns/day) (hour/ns) Performance: 66.258 0.362 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (299 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.155 0.078 198.6 (ns/day) (hour/ns) Performance: 18.862 1.272 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.094 0.047 198.4 (ns/day) (hour/ns) Performance: 31.086 0.772 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.011 193.1 (ns/day) (hour/ns) Performance: 137.627 0.174 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.011 192.6 (ns/day) (hour/ns) Performance: 131.697 0.182 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.071 0.036 197.4 (ns/day) (hour/ns) Performance: 40.575 0.591 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead WARNING 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.022 0.012 192.7 (ns/day) (hour/ns) Performance: 126.619 0.190 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (267 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.084 0.043 197.3 (ns/day) (hour/ns) Performance: 34.465 0.696 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.107 0.054 198.6 (ns/day) (hour/ns) Performance: 27.145 0.884 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.097 0.049 198.5 (ns/day) (hour/ns) Performance: 30.069 0.798 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.010 191.3 (ns/day) (hour/ns) Performance: 151.733 0.158 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.025 0.013 193.6 (ns/day) (hour/ns) Performance: 111.939 0.214 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.103 0.052 198.4 (ns/day) (hour/ns) Performance: 28.333 0.847 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (293 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.067 0.034 196.9 (ns/day) (hour/ns) Performance: 43.277 0.555 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.348 0.174 199.6 (ns/day) (hour/ns) Performance: 8.430 2.847 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.031 0.016 195.4 (ns/day) (hour/ns) Performance: 92.379 0.260 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.075 0.038 197.8 (ns/day) (hour/ns) Performance: 38.648 0.621 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.015 194.3 (ns/day) (hour/ns) Performance: 101.055 0.237 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.048 0.025 196.4 (ns/day) (hour/ns) Performance: 59.873 0.401 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (375 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.102 0.052 197.9 (ns/day) (hour/ns) Performance: 28.470 0.843 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.046 0.023 196.8 (ns/day) (hour/ns) Performance: 62.565 0.384 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.014 194.7 (ns/day) (hour/ns) Performance: 103.761 0.231 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.075 0.038 197.8 (ns/day) (hour/ns) Performance: 38.638 0.621 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.015 194.3 (ns/day) (hour/ns) Performance: 96.070 0.250 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = 2 Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.014 194.2 (ns/day) (hour/ns) Performance: 102.161 0.235 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (232 ms) [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.097 0.049 197.7 (ns/day) (hour/ns) Performance: 30.004 0.800 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.015 194.8 (ns/day) (hour/ns) Performance: 96.649 0.248 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.025 0.013 194.1 (ns/day) (hour/ns) Performance: 115.710 0.207 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.096 0.049 198.2 (ns/day) (hour/ns) Performance: 30.241 0.794 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.025 0.013 193.4 (ns/day) (hour/ns) Performance: 111.558 0.215 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 2 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.012 192.0 (ns/day) (hour/ns) Performance: 125.016 0.192 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (223 ms) [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (16022 ms total) [----------] Global test environment tear-down [==========] 25 tests from 1 test suite ran. (16076 ms total) [ PASSED ] 25 tests. Test time = 16.86 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationCouplingTestsTwoRanks" end time: Feb 22 23:30 EST "MdrunMpiCoordinationCouplingTestsTwoRanks" time elapsed: 00:00:16 ---------------------------------------------------------- 81/90 Testing: MdrunMpiCoordinationConstraintsTestsOneRank 81/90 Test: MdrunMpiCoordinationConstraintsTestsOneRank Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "1" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-constraints-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsOneRank.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationConstraintsTestsOneRank" start time: Feb 22 23:30 EST Output: ---------------------------------------------------------- [==========] Running 13 tests from 1 test suite. [----------] Global test environment set-up. [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.183 2.183 100.0 (ns/day) (hour/ns) Performance: 0.673 35.668 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.4 (ns/day) (hour/ns) Performance: 82.352 0.291 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.018 99.4 (ns/day) (hour/ns) Performance: 83.451 0.288 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.020 99.1 (ns/day) (hour/ns) Performance: 73.726 0.326 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.021 99.1 (ns/day) (hour/ns) Performance: 71.477 0.336 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.015 98.7 (ns/day) (hour/ns) Performance: 100.435 0.239 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3032 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.056 0.057 99.7 (ns/day) (hour/ns) Performance: 25.941 0.925 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.026 0.026 99.6 (ns/day) (hour/ns) Performance: 55.988 0.429 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.3 (ns/day) (hour/ns) Performance: 87.338 0.275 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.044 0.045 99.2 (ns/day) (hour/ns) Performance: 32.882 0.730 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.0 (ns/day) (hour/ns) Performance: 79.527 0.302 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 98.9 (ns/day) (hour/ns) Performance: 81.192 0.296 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (941 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.051 0.051 99.6 (ns/day) (hour/ns) Performance: 28.822 0.833 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.070 0.070 99.8 (ns/day) (hour/ns) Performance: 20.850 1.151 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.054 0.054 99.8 (ns/day) (hour/ns) Performance: 27.167 0.883 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.029 99.3 (ns/day) (hour/ns) Performance: 50.315 0.477 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.020 99.0 (ns/day) (hour/ns) Performance: 74.380 0.323 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.043 0.043 99.5 (ns/day) (hour/ns) Performance: 34.149 0.703 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1035 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.033 99.4 (ns/day) (hour/ns) Performance: 45.067 0.533 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.4 (ns/day) (hour/ns) Performance: 78.921 0.304 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.020 99.4 (ns/day) (hour/ns) Performance: 74.499 0.322 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.124 0.124 99.8 (ns/day) (hour/ns) Performance: 11.857 2.024 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 1.376 1.377 100.0 (ns/day) (hour/ns) Performance: 1.067 22.493 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.024 0.024 99.2 (ns/day) (hour/ns) Performance: 60.660 0.396 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2513 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.024 0.024 99.2 (ns/day) (hour/ns) Performance: 60.172 0.399 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.028 99.6 (ns/day) (hour/ns) Performance: 51.889 0.463 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.3 (ns/day) (hour/ns) Performance: 93.104 0.258 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.487 0.488 100.0 (ns/day) (hour/ns) Performance: 3.012 7.969 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.453 0.453 100.0 (ns/day) (hour/ns) Performance: 3.242 7.402 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.024 0.024 99.2 (ns/day) (hour/ns) Performance: 61.539 0.390 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1782 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.055 0.056 99.7 (ns/day) (hour/ns) Performance: 26.389 0.909 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.118 0.118 99.9 (ns/day) (hour/ns) Performance: 12.456 1.927 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.030 99.6 (ns/day) (hour/ns) Performance: 49.081 0.489 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.072 0.072 99.7 (ns/day) (hour/ns) Performance: 20.274 1.184 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.0 (ns/day) (hour/ns) Performance: 79.493 0.302 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.979 2.979 100.0 (ns/day) (hour/ns) Performance: 0.493 48.684 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4072 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.150 0.150 99.9 (ns/day) (hour/ns) Performance: 9.800 2.449 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.639 4.639 100.0 (ns/day) (hour/ns) Performance: 0.317 75.804 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.055 0.055 99.8 (ns/day) (hour/ns) Performance: 26.470 0.907 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.030 99.4 (ns/day) (hour/ns) Performance: 49.662 0.483 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.1 (ns/day) (hour/ns) Performance: 75.892 0.316 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.014 98.8 (ns/day) (hour/ns) Performance: 102.239 0.235 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5662 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.014 0.015 98.7 (ns/day) (hour/ns) Performance: 100.247 0.239 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.033 99.7 (ns/day) (hour/ns) Performance: 44.911 0.534 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.4 (ns/day) (hour/ns) Performance: 82.472 0.291 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.036 0.037 99.5 (ns/day) (hour/ns) Performance: 40.112 0.598 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.033 99.4 (ns/day) (hour/ns) Performance: 44.328 0.541 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.023 0.023 99.2 (ns/day) (hour/ns) Performance: 63.221 0.380 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (962 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.033 99.4 (ns/day) (hour/ns) Performance: 45.069 0.533 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.026 0.026 99.6 (ns/day) (hour/ns) Performance: 56.768 0.423 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.029 0.029 99.6 (ns/day) (hour/ns) Performance: 50.921 0.471 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.103 0.103 99.8 (ns/day) (hour/ns) Performance: 14.271 1.682 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.200 0.200 99.9 (ns/day) (hour/ns) Performance: 7.349 3.266 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.056 0.056 99.7 (ns/day) (hour/ns) Performance: 26.089 0.920 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1199 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.043 0.043 99.9 (ns/day) (hour/ns) Performance: 34.072 0.704 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.030 0.030 100.0 (ns/day) (hour/ns) Performance: 49.402 0.486 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.9 (ns/day) (hour/ns) Performance: 77.316 0.310 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.027 0.027 99.9 (ns/day) (hour/ns) Performance: 53.964 0.445 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.150 0.150 100.0 (ns/day) (hour/ns) Performance: 9.791 2.451 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.9 (ns/day) (hour/ns) Performance: 82.029 0.293 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1047 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.233 0.234 100.0 (ns/day) (hour/ns) Performance: 6.290 3.816 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.082 0.082 100.0 (ns/day) (hour/ns) Performance: 17.984 1.335 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.021 0.021 99.9 (ns/day) (hour/ns) Performance: 69.189 0.347 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.033 100.0 (ns/day) (hour/ns) Performance: 44.667 0.537 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.017 0.017 99.9 (ns/day) (hour/ns) Performance: 85.336 0.281 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.025 0.025 99.9 (ns/day) (hour/ns) Performance: 57.950 0.414 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1160 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.110 0.110 100.0 (ns/day) (hour/ns) Performance: 13.384 1.793 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.032 0.032 99.9 (ns/day) (hour/ns) Performance: 45.482 0.528 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.047 0.047 100.0 (ns/day) (hour/ns) Performance: 31.473 0.763 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.059 0.059 100.0 (ns/day) (hour/ns) Performance: 24.796 0.968 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.038 0.038 100.0 (ns/day) (hour/ns) Performance: 38.826 0.618 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.9 (ns/day) (hour/ns) Performance: 80.041 0.300 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1053 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.034 0.034 99.9 (ns/day) (hour/ns) Performance: 43.621 0.550 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.035 0.035 99.9 (ns/day) (hour/ns) Performance: 42.383 0.566 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.018 0.018 99.9 (ns/day) (hour/ns) Performance: 82.935 0.289 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.026 0.026 99.9 (ns/day) (hour/ns) Performance: 55.851 0.430 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.016 0.016 99.9 (ns/day) (hour/ns) Performance: 91.860 0.261 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.019 0.019 99.9 (ns/day) (hour/ns) Performance: 79.214 0.303 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (911 ms) [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (25377 ms total) [----------] Global test environment tear-down [==========] 13 tests from 1 test suite ran. (25419 ms total) [ PASSED ] 13 tests. Test time = 26.12 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationConstraintsTestsOneRank" end time: Feb 22 23:31 EST "MdrunMpiCoordinationConstraintsTestsOneRank" time elapsed: 00:00:26 ---------------------------------------------------------- 82/90 Testing: MdrunMpiCoordinationConstraintsTestsTwoRanks 82/90 Test: MdrunMpiCoordinationConstraintsTestsTwoRanks Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-mpi-coordination-constraints-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsTwoRanks.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunMpiCoordinationConstraintsTestsTwoRanks" start time: Feb 22 23:31 EST Output: ---------------------------------------------------------- [==========] Running 13 tests from 1 test suite. [----------] Global test environment set-up. [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.4%. The balanceable part of the MD step is 23%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 3.277 1.639 200.0 (ns/day) (hour/ns) Performance: 0.896 26.775 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 29%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.083 0.042 199.5 (ns/day) (hour/ns) Performance: 35.115 0.683 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.9%. The balanceable part of the MD step is 44%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.074 0.037 199.3 (ns/day) (hour/ns) Performance: 39.588 0.606 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.6%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.467 0.234 199.8 (ns/day) (hour/ns) Performance: 6.289 3.816 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.9%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 8.512 4.257 200.0 (ns/day) (hour/ns) Performance: 0.345 69.553 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.7%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.298 0.149 199.7 (ns/day) (hour/ns) Performance: 9.848 2.437 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7127 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.6%. The balanceable part of the MD step is 24%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 6.943 3.472 200.0 (ns/day) (hour/ns) Performance: 0.423 56.726 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.9%. The balanceable part of the MD step is 28%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 44.682 22.341 200.0 (ns/day) (hour/ns) Performance: 0.066 365.055 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 2.0%. The balanceable part of the MD step is 47%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.121 0.560 200.0 (ns/day) (hour/ns) Performance: 2.621 9.158 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 4.255 2.128 200.0 (ns/day) (hour/ns) Performance: 0.690 34.768 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.9%. The balanceable part of the MD step is 31%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 1.302 0.651 199.9 (ns/day) (hour/ns) Performance: 2.256 10.638 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 35%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.107 0.053 199.2 (ns/day) (hour/ns) Performance: 27.459 0.874 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (29974 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.5%. The balanceable part of the MD step is 23%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.191 0.096 199.6 (ns/day) (hour/ns) Performance: 15.338 1.565 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 28%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.070 0.035 199.3 (ns/day) (hour/ns) Performance: 41.897 0.573 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.8%. The balanceable part of the MD step is 46%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.8%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.040 0.020 198.7 (ns/day) (hour/ns) Performance: 73.016 0.329 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 35%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.044 0.022 198.2 (ns/day) (hour/ns) Performance: 65.437 0.367 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.5%. The balanceable part of the MD step is 34%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.042 0.021 198.1 (ns/day) (hour/ns) Performance: 68.746 0.349 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 35%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.5%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.037 0.019 197.9 (ns/day) (hour/ns) Performance: 77.650 0.309 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (981 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.103 0.052 199.1 (ns/day) (hour/ns) Performance: 28.347 0.847 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.087 0.043 199.4 (ns/day) (hour/ns) Performance: 33.792 0.710 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.020 0.010 197.6 (ns/day) (hour/ns) Performance: 146.412 0.164 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.047 0.024 198.3 (ns/day) (hour/ns) Performance: 61.868 0.388 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.041 0.021 198.0 (ns/day) (hour/ns) Performance: 71.573 0.335 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.045 0.022 198.2 (ns/day) (hour/ns) Performance: 65.383 0.367 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (932 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.078 0.039 198.6 (ns/day) (hour/ns) Performance: 37.369 0.642 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.059 0.030 199.2 (ns/day) (hour/ns) Performance: 49.737 0.483 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.095 0.048 199.5 (ns/day) (hour/ns) Performance: 30.699 0.782 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.063 0.032 198.7 (ns/day) (hour/ns) Performance: 46.087 0.521 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.048 0.024 198.3 (ns/day) (hour/ns) Performance: 60.617 0.396 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 4.577 2.289 200.0 (ns/day) (hour/ns) Performance: 0.642 37.395 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3381 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.685 1.343 200.0 (ns/day) (hour/ns) Performance: 1.094 21.945 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.177 0.089 199.7 (ns/day) (hour/ns) Performance: 16.595 1.446 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.099 0.049 199.5 (ns/day) (hour/ns) Performance: 29.746 0.807 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.017 197.5 (ns/day) (hour/ns) Performance: 87.846 0.273 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.043 0.021 198.2 (ns/day) (hour/ns) Performance: 68.388 0.351 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.031 0.016 197.4 (ns/day) (hour/ns) Performance: 93.655 0.256 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2291 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.328 0.164 199.7 (ns/day) (hour/ns) Performance: 8.950 2.682 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.106 0.053 199.5 (ns/day) (hour/ns) Performance: 27.559 0.871 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.033 0.016 198.5 (ns/day) (hour/ns) Performance: 89.278 0.269 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.247 0.124 199.7 (ns/day) (hour/ns) Performance: 11.865 2.023 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.171 0.086 199.5 (ns/day) (hour/ns) Performance: 17.168 1.398 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.044 0.022 198.2 (ns/day) (hour/ns) Performance: 66.184 0.363 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1279 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.078 0.039 198.9 (ns/day) (hour/ns) Performance: 37.572 0.639 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 3.210 1.605 200.0 (ns/day) (hour/ns) Performance: 0.915 26.228 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.276 0.138 199.8 (ns/day) (hour/ns) Performance: 10.640 2.256 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.057 0.029 198.6 (ns/day) (hour/ns) Performance: 51.260 0.468 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.160 0.080 199.5 (ns/day) (hour/ns) Performance: 18.369 1.307 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.117 0.059 199.3 (ns/day) (hour/ns) Performance: 24.956 0.962 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2717 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.317 0.159 199.7 (ns/day) (hour/ns) Performance: 9.253 2.594 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.143 0.071 199.7 (ns/day) (hour/ns) Performance: 20.561 1.167 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.041 0.021 198.8 (ns/day) (hour/ns) Performance: 71.559 0.335 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 2.774 1.387 200.0 (ns/day) (hour/ns) Performance: 1.059 22.666 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.076 0.038 199.0 (ns/day) (hour/ns) Performance: 38.482 0.624 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.039 0.020 198.0 (ns/day) (hour/ns) Performance: 74.624 0.322 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2455 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.2%. The balanceable part of the MD step is 23%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.0%. Core t (s) Wall t (s) (%) Time: 0.080 0.041 197.3 (ns/day) (hour/ns) Performance: 36.088 0.665 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.9%. The balanceable part of the MD step is 30%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. Core t (s) Wall t (s) (%) Time: 0.141 0.071 198.8 (ns/day) (hour/ns) Performance: 20.750 1.157 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.6%. The balanceable part of the MD step is 54%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. Core t (s) Wall t (s) (%) Time: 0.041 0.021 196.3 (ns/day) (hour/ns) Performance: 71.160 0.337 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.6%. The balanceable part of the MD step is 39%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. Core t (s) Wall t (s) (%) Time: 0.047 0.024 196.5 (ns/day) (hour/ns) Performance: 61.192 0.392 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 39%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. Core t (s) Wall t (s) (%) Time: 0.270 0.136 199.2 (ns/day) (hour/ns) Performance: 10.827 2.217 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 4. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 4. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.7%. The balanceable part of the MD step is 39%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. Core t (s) Wall t (s) (%) Time: 0.155 0.078 198.9 (ns/day) (hour/ns) Performance: 18.878 1.271 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1130 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.2%. The balanceable part of the MD step is 15%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.0%. Core t (s) Wall t (s) (%) Time: 0.196 0.098 198.9 (ns/day) (hour/ns) Performance: 14.919 1.609 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.5%. The balanceable part of the MD step is 29%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.1%. Core t (s) Wall t (s) (%) Time: 0.053 0.027 197.2 (ns/day) (hour/ns) Performance: 54.572 0.440 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.5%. The balanceable part of the MD step is 54%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. Core t (s) Wall t (s) (%) Time: 0.031 0.016 195.3 (ns/day) (hour/ns) Performance: 92.025 0.261 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.7%. The balanceable part of the MD step is 40%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.3%. Core t (s) Wall t (s) (%) Time: 0.070 0.036 197.6 (ns/day) (hour/ns) Performance: 41.254 0.582 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 0.6%. The balanceable part of the MD step is 42%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.2%. Core t (s) Wall t (s) (%) Time: 0.037 0.019 195.6 (ns/day) (hour/ns) Performance: 76.920 0.312 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.1%. The balanceable part of the MD step is 40%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.4%. Core t (s) Wall t (s) (%) Time: 0.030 0.016 194.6 (ns/day) (hour/ns) Performance: 94.602 0.254 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (970 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.380 0.191 199.4 (ns/day) (hour/ns) Performance: 7.698 3.118 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5.021 2.511 200.0 (ns/day) (hour/ns) Performance: 0.585 41.033 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.261 0.131 199.4 (ns/day) (hour/ns) Performance: 11.241 2.135 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.051 0.026 196.5 (ns/day) (hour/ns) Performance: 56.107 0.428 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.043 0.022 195.9 (ns/day) (hour/ns) Performance: 67.272 0.357 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: COM removal frequency is set to (5). Other settings require a global communication frequency of 2. Note that this will require additional global communication steps, which will reduce performance when using multiple ranks. Consider setting nstcomm to a multiple of 2. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.045 0.023 196.3 (ns/day) (hour/ns) Performance: 63.389 0.379 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3666 ms) [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.097 0.049 197.7 (ns/day) (hour/ns) Performance: 30.066 0.798 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (1) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.036 0.018 195.8 (ns/day) (hour/ns) Performance: 79.689 0.301 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.028 0.014 194.5 (ns/day) (hour/ns) Performance: 103.043 0.233 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.044 0.022 196.1 (ns/day) (hour/ns) Performance: 65.402 0.367 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.057 0.029 196.9 (ns/day) (hour/ns) Performance: 51.129 0.469 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider setting nstcomm equal to nstcalcenergy for less overhead Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.140 0.070 198.7 (ns/day) (hour/ns) Performance: 20.919 1.147 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (967 ms) [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (57877 ms total) [----------] Global test environment tear-down [==========] 13 tests from 1 test suite ran. (57931 ms total) [ PASSED ] 13 tests. Test time = 58.72 sec ---------------------------------------------------------- Test Passed. "MdrunMpiCoordinationConstraintsTestsTwoRanks" end time: Feb 22 23:32 EST "MdrunMpiCoordinationConstraintsTestsTwoRanks" time elapsed: 00:00:58 ---------------------------------------------------------- 83/90 Testing: MdrunFEPTests 83/90 Test: MdrunFEPTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-fep-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunFEPTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunFEPTests" start time: Feb 22 23:32 EST Output: ---------------------------------------------------------- [==========] Running 10 tests from 1 test suite. [----------] Global test environment set-up. [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s NOTE 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used WARNING 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 355.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. NOTE 3 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: For free energy simulations, the optimal load limit increases from 0.5 to 0.667 There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'AA' 20 steps, 0.0 ps. Setting the LD random seed to -1745035314 Generated 153 of the 153 non-bonded parameter combinations Generated 153 of the 153 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ASN' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'ASN' Analysing residue names: There are: 1 Protein residues There are: 56 Water residues Analysing Protein... The largest distance between non-perturbed excluded atoms is 0.164 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.94 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 50.578 25.289 200.0 (ns/day) (hour/ns) Performance: 0.072 334.516 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (25934 ms) [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s NOTE 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used WARNING 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 355.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. NOTE 3 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: For free energy simulations, the optimal load limit increases from 0.5 to 0.667 There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'AA' 20 steps, 0.0 ps. Setting the LD random seed to -1108452755 Generated 153 of the 153 non-bonded parameter combinations Generated 153 of the 153 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ASN' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'ASN' Analysing residue names: There are: 1 Protein residues There are: 56 Water residues Analysing Protein... The largest distance between non-perturbed excluded atoms is 0.164 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.94 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 22.999 11.500 200.0 (ns/day) (hour/ns) Performance: 0.158 152.112 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (11957 ms) [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s NOTE 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used NOTE 2 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. WARNING 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 355.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. NOTE 4 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: For free energy simulations, the optimal load limit increases from 0.5 to 0.667 There were 4 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'AA' 20 steps, 0.0 ps. Setting the LD random seed to -537155475 Generated 153 of the 153 non-bonded parameter combinations Generated 153 of the 153 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ASN' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'ASN' Analysing residue names: There are: 1 Protein residues There are: 56 Water residues Analysing Protein... The largest distance between non-perturbed excluded atoms is 0.164 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.94 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 34.924 17.462 200.0 (ns/day) (hour/ns) Performance: 0.104 230.984 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (17910 ms) [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s NOTE 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off and vdw_modifier=Force-switch WARNING 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 355.00 NOTE 2 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. NOTE 3 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: For free energy simulations, the optimal load limit increases from 0.5 to 0.667 There were 3 notes There was 1 warning Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'AA' 100 steps, 0.1 ps. Setting the LD random seed to -1075937793 Generated 153 of the 153 non-bonded parameter combinations Generated 153 of the 153 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ASN' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'ASN' Analysing residue names: There are: 1 Protein residues There are: 56 Water residues Analysing Protein... The largest distance between non-perturbed excluded atoms is 0.164 nm Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 Estimate for the relative computational load of the PME mesh part: 0.94 This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 117.198 58.599 200.0 (ns/day) (hour/ns) Performance: 0.149 161.164 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (58862 ms) [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s WARNING 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution, and should not be used for new production simulations (in our opinion). We would recommend the V-rescale thermostat. Generating 1-4 interactions: fudge = 0.5 WARNING 2 [file topol.top, line 72]: No default Bond types for perturbed atoms, using normal values WARNING 3 [file topol.top, line 73]: No default Bond types for perturbed atoms, using normal values WARNING 4 [file topol.top, line 98]: No default Angle types for perturbed atoms, using normal values WARNING 5 [file topol.top, line 99]: No default Angle types for perturbed atoms, using normal values WARNING 6 [file topol.top, line 100]: No default Angle types for perturbed atoms, using normal values WARNING 7 [file topol.top, line 101]: No default Angle types for perturbed atoms, using normal values WARNING 8 [file topol.top, line 111]: No default Ryckaert-Bell. types for perturbed atoms, using normal values WARNING 9 [file topol.top, line 112]: No default Ryckaert-Bell. types for perturbed atoms, using normal values WARNING 10 [file topol.top, line 113]: No default Ryckaert-Bell. types for perturbed atoms, using normal values WARNING 11 [file topol.top, line 114]: No default Ryckaert-Bell. types for perturbed atoms, using normal values Number of degrees of freedom in T-Coupling group System is 355.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. NOTE 2 [file ${WORKDIR}/gromacs-2022/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: For free energy simulations, the optimal load limit increases from 0.5 to 0.667 There were 2 notes There were 11 warnings Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2022 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'AA' 20 steps, 0.0 ps. Test time = 119.83 sec ---------------------------------------------------------- Test Failed. "MdrunFEPTests" end time: Feb 22 23:34 EST "MdrunFEPTests" time elapsed: 00:01:59 ---------------------------------------------------------- 84/90 Testing: MdrunPullTests 84/90 Test: MdrunPullTests Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-pull-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunPullTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunPullTests" start time: Feb 22 23:34 EST Output: ---------------------------------------------------------- [==========] Running 4 tests from 1 test suite. [----------] Global test environment set-up. [----------] 4 tests from PullTest/PullIntegrationTest [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 Generating 1-4 interactions: fudge = 0.5 Pull group 1 'r_1' has 3 atoms Pull group 2 'r_2' has 3 atoms Number of degrees of freedom in T-Coupling group System is 1293.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 303.122 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 0.575 nm 0.600 nm There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 20 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 11.312 5.656 200.0 (ns/day) (hour/ns) Performance: 0.321 74.820 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (8083 ms) [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 Generating 1-4 interactions: fudge = 0.5 Pull group 1 'r_1' has 3 atoms Pull group 2 'r_2' has 3 atoms Number of degrees of freedom in T-Coupling group System is 1293.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 303.122 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 0.301 nm 0.400 nm There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 20 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 9.972 4.986 200.0 (ns/day) (hour/ns) Performance: 0.364 65.959 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (5244 ms) [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 Generating 1-4 interactions: fudge = 0.5 Pull group 1 'r_1' has 3 atoms Pull group 2 'r_2' has 3 atoms Pull group 3 'r_3' has 3 atoms Number of degrees of freedom in T-Coupling group System is 1292.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 303.357 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 0.575 nm 0.500 nm 1 3 2 3 3 8 0.331 nm 0.400 nm There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 20 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 13.676 6.838 200.0 (ns/day) (hour/ns) Performance: 0.265 90.452 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (7085 ms) [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 Generating 1-4 interactions: fudge = 0.5 Pull group 1 'r_1' has 3 atoms Pull group 2 'r_2' has 3 atoms Number of degrees of freedom in T-Coupling group System is 1293.00 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 303.122 K for determining the Verlet buffer size Pull group natoms pbc atom distance at start reference at t=0 1 3 2 2 3 5 0.575 nm 0.000 nm 1 3 2 2 3 5 0.050 nm 0.000 nm There was 1 note Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Non-default thread affinity set, disabling internal thread affinity Using 2 OpenMP threads starting mdrun 'spc2' 20 steps, 0.0 ps. Generated 330891 of the 330891 non-bonded parameter combinations Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data Writing final coordinates. Core t (s) Wall t (s) (%) Time: 11.111 5.556 200.0 (ns/day) (hour/ns) Performance: 0.327 73.492 Opened ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (5798 ms) [----------] 4 tests from PullTest/PullIntegrationTest (26212 ms total) [----------] Global test environment tear-down [==========] 4 tests from 1 test suite ran. (26255 ms total) [ PASSED ] 4 tests. Test time = 26.95 sec ---------------------------------------------------------- Test Passed. "MdrunPullTests" end time: Feb 22 23:34 EST "MdrunPullTests" time elapsed: 00:00:26 ---------------------------------------------------------- 85/90 Testing: MdrunSimulatorComparison 85/90 Test: MdrunSimulatorComparison Command: "${WORKDIR}/gromacs-2022/build/bin/mdrun-simulator-comparison-test" "-ntomp" "2" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunSimulatorComparison.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunSimulatorComparison" start time: Feb 22 23:34 EST Output: ---------------------------------------------------------- [==========] Running 0 tests from 0 test suites. [==========] 0 tests from 0 test suites ran. (0 ms total) [ PASSED ] 0 tests. YOU HAVE 82 DISABLED TESTS Test time = 0.69 sec ---------------------------------------------------------- Test Passed. "MdrunSimulatorComparison" end time: Feb 22 23:34 EST "MdrunSimulatorComparison" time elapsed: 00:00:00 ---------------------------------------------------------- 86/90 Testing: MdrunVirtualSiteTests 86/90 Test: MdrunVirtualSiteTests Command: "${OPENMPI_PREFIX}/bin/mpiexec" "-n" "2" "${WORKDIR}/gromacs-2022/build/bin/mdrun-vsites-test" "--gtest_output=xml:${WORKDIR}/gromacs-2022/build/Testing/Temporary/MdrunVirtualSiteTests.xml" Directory: ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests "MdrunVirtualSiteTests" start time: Feb 22 23:34 EST Output: ---------------------------------------------------------- [==========] Running 37 tests from 2 test suites. [----------] Global test environment set-up. [----------] 1 test from VirtualSiteVelocityTest [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) [----------] 1 test from VirtualSiteVelocityTest (0 ms total) [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.3%. The balanceable part of the MD step is 16%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 10.932 5.466 200.0 (ns/day) (hour/ns) Performance: 0.142 168.715 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading virtual site types... trr version: GMX_trn_file (single precision) trr version: GMX_trn_file (single precision) [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (5489 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 6.4%. The balanceable part of the MD step is 13%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.9%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.321 0.161 199.7 (ns/day) (hour/ns) Performance: 4.843 4.956 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (180 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 14.9%. The balanceable part of the MD step is 9%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.3%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.143 0.071 199.4 (ns/day) (hour/ns) Performance: 10.882 2.205 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (87 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.505 0.253 199.8 (ns/day) (hour/ns) Performance: 3.078 7.798 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (269 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 18.812 9.406 200.0 (ns/day) (hour/ns) Performance: 0.083 290.308 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (9423 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.760 0.380 199.9 (ns/day) (hour/ns) Performance: 2.044 11.739 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (400 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.845 0.423 199.9 (ns/day) (hour/ns) Performance: 1.839 13.048 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (439 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.086 0.043 199.0 (ns/day) (hour/ns) Performance: 18.093 1.326 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (59 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 5 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.087 0.044 199.0 (ns/day) (hour/ns) Performance: 17.804 1.348 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (60 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 13.3%. The balanceable part of the MD step is 9%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.3%. NOTE: 50 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.153 0.077 199.4 (ns/day) (hour/ns) Performance: 10.112 2.373 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (92 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2022 (single precision) Can not increase nstlist because an NVE ensemble is used Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 5.7%. The balanceable part of the MD step is 11%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 0.6%. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.060 0.030 198.5 (ns/day) (hour/ns) Performance: 25.718 0.933 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (49 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.078 0.039 198.9 (ns/day) (hour/ns) Performance: 19.826 1.211 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (55 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.031 0.016 197.3 (ns/day) (hour/ns) Performance: 49.059 0.489 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (32 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 49 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.076 0.038 198.9 (ns/day) (hour/ns) Performance: 20.251 1.185 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (54 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.028 0.014 197.1 (ns/day) (hour/ns) Performance: 54.018 0.444 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (30 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.032 0.016 197.5 (ns/day) (hour/ns) Performance: 48.275 0.497 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (32 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.023 0.012 196.3 (ns/day) (hour/ns) Performance: 66.168 0.363 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (28 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.024 0.012 196.7 (ns/day) (hour/ns) Performance: 63.919 0.375 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (28 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.026 0.013 196.8 (ns/day) (hour/ns) Performance: 59.903 0.401 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (29 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes This run will generate roughly 0 Mb of data Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.022 0.011 196.4 (ns/day) (hour/ns) Performance: 68.465 0.351 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (27 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 NOTE 1 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Number of degrees of freedom in T-Coupling group System is 45.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 3 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: There are 6 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data NOTE 4 [file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 4 notes Highest SIMD level supported by all nodes in run: AVX2_256 SIMD instructions selected at compile time: AVX2_128 Compiled SIMD newer than supported; program might crash. Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022 (single precision) Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 Using 2 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process starting mdrun 'Virtual sites test system in vacuo' 8 steps, 0.0 ps. Writing final coordinates. NOTE: 48 % of the run time was spent communicating energies, you might want to increase some nst* mdp options Core t (s) Wall t (s) (%) Time: 0.030 0.015 197.3 (ns/day) (hour/ns) Performance: 50.839 0.472 Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022 (single precision) Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022 (single precision) Reading virtual site types... Reading file ${WORKDIR}/gromacs-2022/build/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022 (single precision) Reading virtual site types... [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (31 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (16915 ms total) [----------] Global test environment tear-down [==========] 37 tests from 2 test suites ran. (16971 ms total) [ PASSED ] 37 tests. Test time = 17.80 sec ---------------------------------------------------------- Test Passed. "MdrunVirtualSiteTests" end time: Feb 22 23:34 EST "MdrunVirtualSiteTests" time elapsed: 00:00:17 ---------------------------------------------------------- 87/90 Testing: regressiontests/complex 87/90 Test: regressiontests/complex Command: "/usr/bin/perl" "${WORKDIR}/regressiontests-2022/gmxtest.pl" "complex" "-np" "8" "-mpirun" "${OPENMPI_PREFIX}/bin/mpiexec" "-suffix" "_mpi" "-crosscompile" "-noverbose" "-nosuffix" Directory: ${WORKDIR}/gromacs-2022/build/tests "regressiontests/complex" start time: Feb 22 23:34 EST Output: ---------------------------------------------------------- Will test on 8 MPI ranks (if possible) Will test using executable suffix _mpi All 48 complex tests PASSED Test time = 843.19 sec ---------------------------------------------------------- Test Passed. "regressiontests/complex" end time: Feb 22 23:48 EST "regressiontests/complex" time elapsed: 00:14:03 ---------------------------------------------------------- 88/90 Testing: regressiontests/freeenergy 88/90 Test: regressiontests/freeenergy Command: "/usr/bin/perl" "${WORKDIR}/regressiontests-2022/gmxtest.pl" "freeenergy" "-np" "8" "-mpirun" "${OPENMPI_PREFIX}/bin/mpiexec" "-suffix" "_mpi" "-crosscompile" "-noverbose" "-nosuffix" Directory: ${WORKDIR}/gromacs-2022/build/tests "regressiontests/freeenergy" start time: Feb 22 23:48 EST Output: ---------------------------------------------------------- Will test on 8 MPI ranks (if possible) Will test using executable suffix _mpi All 10 freeenergy tests PASSED Test time = 155.10 sec ---------------------------------------------------------- Test Passed. "regressiontests/freeenergy" end time: Feb 22 23:51 EST "regressiontests/freeenergy" time elapsed: 00:02:35 ---------------------------------------------------------- 89/90 Testing: regressiontests/rotation 89/90 Test: regressiontests/rotation Command: "/usr/bin/perl" "${WORKDIR}/regressiontests-2022/gmxtest.pl" "rotation" "-np" "8" "-mpirun" "${OPENMPI_PREFIX}/bin/mpiexec" "-suffix" "_mpi" "-crosscompile" "-noverbose" "-nosuffix" Directory: ${WORKDIR}/gromacs-2022/build/tests "regressiontests/rotation" start time: Feb 22 23:51 EST Output: ---------------------------------------------------------- Will test on 8 MPI ranks (if possible) Will test using executable suffix _mpi All 12 rotation tests PASSED Test time = 216.87 sec ---------------------------------------------------------- Test Passed. "regressiontests/rotation" end time: Feb 22 23:55 EST "regressiontests/rotation" time elapsed: 00:03:36 ---------------------------------------------------------- 90/90 Testing: regressiontests/essentialdynamics 90/90 Test: regressiontests/essentialdynamics Command: "/usr/bin/perl" "${WORKDIR}/regressiontests-2022/gmxtest.pl" "essentialdynamics" "-np" "8" "-mpirun" "${OPENMPI_PREFIX}/bin/mpiexec" "-suffix" "_mpi" "-crosscompile" "-noverbose" "-nosuffix" Directory: ${WORKDIR}/gromacs-2022/build/tests "regressiontests/essentialdynamics" start time: Feb 22 23:55 EST Output: ---------------------------------------------------------- Will test on 8 MPI ranks (if possible) Will test using executable suffix _mpi All 7 essential dynamics tests PASSED Test time = 93.88 sec ---------------------------------------------------------- Test Passed. "regressiontests/essentialdynamics" end time: Feb 22 23:56 EST "regressiontests/essentialdynamics" time elapsed: 00:01:33 ---------------------------------------------------------- End testing: Feb 22 23:56 EST GTest = 897.04 sec*proc IntegrationTest = 654.33 sec*proc MpiTest = 330.03 sec*proc SlowTest = 160.03 sec*proc UnitTest = 82.67 sec*proc