Test project /userhome/braden/software/gromacs-2022.5/buil Start 62: MdrunIOTests 1/1 Test #62: MdrunIOTests .....................***Failed 17.64 sec [==========] Running 66 tests from 13 test suites. [----------] Global test environment set-up. [----------] 5 tests from GromppTest [ RUN ] GromppTest.EmptyMdpFileWorks NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 2113402845 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 (22 ms) [ RUN ] GromppTest.SimulatedAnnealingWorks NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 -50663465 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 (20 ms) [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 -541499461 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 (19 ms) [ RUN ] GromppTest.ValidTransformationCoord NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 -1108213761 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 (35 ms) [ RUN ] GromppTest.InvalidTransformationCoord NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 -168296834 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 (84 ms) [----------] 5 tests from GromppTest (183 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -167920641 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: 0.198 0.099 199.2 (ns/day) (hour/ns) Performance: 2.615 9.179 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5 (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 unknown file: Failure C++ exception with description "File locking is not supported on this system. Use mdrun -noappend to restart." thrown in the test body. [ FAILED ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (168 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 1, rlist from 1.024 to 1 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 100 steps, 0.1 ps. Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps Setting the LD random seed to -335544594 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 Core t (s) Wall t (s) (%) Time: 0.092 0.047 198.8 (ns/day) (hour/ns) Performance: 5.571 4.308 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5 (single precision) Setting nsteps to 102 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 unknown file: Failure C++ exception with description "File locking is not supported on this system. Use mdrun -noappend to restart." thrown in the test body. [ FAILED ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (99 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to 2011167983 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: 0.123 0.061 199.3 (ns/day) (hour/ns) Performance: 4.216 5.693 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Setting nsteps to 4 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.125 0.063 199.2 (ns/day) (hour/ns) Performance: 4.122 5.822 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Setting nsteps to 6 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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. Core t (s) Wall t (s) (%) Time: 0.128 0.064 199.2 (ns/day) (hour/ns) Performance: 4.023 5.965 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Setting nsteps to 8 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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. Core t (s) Wall t (s) (%) Time: 0.053 0.027 198.7 (ns/day) (hour/ns) Performance: 9.635 2.491 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). Core t (s) Wall t (s) (%) Time: 0.001 0.001 157.3 (ns/day) (hour/ns) Performance: 102.283 0.235 [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (354 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -1210458497 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: 0.089 0.045 198.1 (ns/day) (hour/ns) Performance: 5.791 4.144 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5 (single precision) Setting nsteps to 4 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.095 0.048 199.0 (ns/day) (hour/ns) Performance: 9.021 2.660 [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (156 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to -966683 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: 0.121 0.061 199.1 (ns/day) (hour/ns) Performance: 4.262 5.632 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5 (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 (103 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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 2 steps, 0.0 ps. Setting the LD random seed to 1593829887 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: 0.101 0.051 198.8 (ns/day) (hour/ns) Performance: 5.100 4.706 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5 (single precision) Setting nsteps to 4 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5 (single precision) Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.096 0.048 199.2 (ns/day) (hour/ns) Performance: 5.399 4.446 [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (169 ms) [----------] 6 tests from MdrunTerminationTest (1051 ms total) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.136 0.068 198.8 (ns/day) (hour/ns) Performance: 21.520 1.115 trr version: GMX_trn_file (single precision) [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (120 ms) [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.163 0.081 199.8 (ns/day) (hour/ns) Performance: 18.030 1.331 [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (122 ms) [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (242 ms total) [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.097 0.049 198.9 (ns/day) (hour/ns) Performance: 30.213 0.794 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.082 0.041 197.7 (ns/day) (hour/ns) Performance: 18.836 1.274 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.249 0.125 199.2 (ns/day) (hour/ns) Performance: 6.219 3.859 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (312 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.121 0.061 199.9 (ns/day) (hour/ns) Performance: 24.248 0.990 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.166 0.083 199.9 (ns/day) (hour/ns) Performance: 9.384 2.557 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.112 0.056 199.8 (ns/day) (hour/ns) Performance: 13.896 1.727 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (283 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.054 0.027 197.2 (ns/day) (hour/ns) Performance: 53.468 0.449 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.058 0.030 197.4 (ns/day) (hour/ns) Performance: 26.325 0.912 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.105 0.053 198.5 (ns/day) (hour/ns) Performance: 14.774 1.625 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (210 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.126 0.063 198.8 (ns/day) (hour/ns) Performance: 23.262 1.032 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.096 0.048 198.6 (ns/day) (hour/ns) Performance: 16.045 1.496 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.141 0.071 198.9 (ns/day) (hour/ns) Performance: 10.985 2.185 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (262 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.071 0.036 197.7 (ns/day) (hour/ns) Performance: 41.157 0.583 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.074 0.037 198.0 (ns/day) (hour/ns) Performance: 20.909 1.148 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.133 0.067 198.9 (ns/day) (hour/ns) Performance: 11.619 2.066 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (260 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.152 0.076 199.9 (ns/day) (hour/ns) Performance: 19.375 1.239 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.094 0.047 199.9 (ns/day) (hour/ns) Performance: 16.527 1.452 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.102 0.051 199.7 (ns/day) (hour/ns) Performance: 15.150 1.584 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (258 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.060 0.030 197.6 (ns/day) (hour/ns) Performance: 48.242 0.497 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.102 0.051 198.4 (ns/day) (hour/ns) Performance: 15.176 1.581 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.064 0.033 197.5 (ns/day) (hour/ns) Performance: 23.916 1.004 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/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 (222 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 /userhome/braden/software/gromacs-2022.5/buil/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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 0.754 nm, buffer size 0.054 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 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 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 0.754 nm, buffer size 0.054 nm Set rlist, assuming 4x4 atom pair-list, to 0.754 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: 0.133 0.067 198.9 (ns/day) (hour/ns) Performance: 21.946 1.094 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.132 0.066 198.8 (ns/day) (hour/ns) Performance: 11.746 2.043 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.205 0.103 199.0 (ns/day) (hour/ns) Performance: 7.564 3.173 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_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/7 (321 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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: 0.072 0.036 197.9 (ns/day) (hour/ns) Performance: 40.411 0.594 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.066 0.034 197.6 (ns/day) (hour/ns) Performance: 23.203 1.034 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.175 0.088 199.0 (ns/day) (hour/ns) Performance: 8.851 2.712 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_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/8 (464 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size NOTE 5 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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: 0.140 0.071 198.5 (ns/day) (hour/ns) Performance: 20.797 1.154 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.096 0.048 198.5 (ns/day) (hour/ns) Performance: 16.121 1.489 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.994 0.498 199.7 (ns/day) (hour/ns) Performance: 1.562 15.366 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_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/9 (725 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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: 0.088 0.044 198.4 (ns/day) (hour/ns) Performance: 33.147 0.724 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.078 0.040 198.1 (ns/day) (hour/ns) Performance: 19.684 1.219 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.112 0.057 198.6 (ns/day) (hour/ns) Performance: 13.758 1.744 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_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/10 (295 ms) [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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: 0.118 0.059 198.7 (ns/day) (hour/ns) Performance: 24.806 0.968 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.106 0.054 198.7 (ns/day) (hour/ns) Performance: 14.516 1.653 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.174 0.088 199.1 (ns/day) (hour/ns) Performance: 8.876 2.704 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_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/11 (314 ms) [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (3932 ms total) [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.069 0.035 196.6 (ns/day) (hour/ns) Performance: 41.622 0.577 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.067 0.034 196.0 (ns/day) (hour/ns) Performance: 22.794 1.053 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.123 0.062 197.9 (ns/day) (hour/ns) Performance: 12.463 1.926 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (269 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 79.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 79.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size NOTE 4 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.177 0.089 199.9 (ns/day) (hour/ns) Performance: 16.579 1.448 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.158 0.079 199.9 (ns/day) (hour/ns) Performance: 9.827 2.442 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.125 0.063 199.7 (ns/day) (hour/ns) Performance: 12.418 1.933 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (342 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 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 0.728 nm, buffer size 0.028 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data 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 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 0.728 nm, buffer size 0.028 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: 0.089 0.045 197.3 (ns/day) (hour/ns) Performance: 32.405 0.741 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.088 0.044 197.4 (ns/day) (hour/ns) Performance: 17.531 1.369 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.117 0.059 198.2 (ns/day) (hour/ns) Performance: 13.189 1.820 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (322 ms) [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 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 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 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.137 0.069 198.3 (ns/day) (hour/ns) Performance: 21.306 1.126 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.128 0.065 198.1 (ns/day) (hour/ns) Performance: 11.994 2.001 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.188 0.095 198.5 (ns/day) (hour/ns) Performance: 8.210 2.923 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_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 ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (355 ms) [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1291 ms total) [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.069 0.035 197.4 (ns/day) (hour/ns) Performance: 41.746 0.575 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.071 0.036 197.9 (ns/day) (hour/ns) Performance: 21.580 1.112 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.104 0.053 198.4 (ns/day) (hour/ns) Performance: 14.769 1.625 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (231 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 There were 2 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 There were 2 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.153 0.077 198.9 (ns/day) (hour/ns) Performance: 19.154 1.253 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.101 0.051 198.3 (ns/day) (hour/ns) Performance: 15.204 1.579 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.112 0.056 198.6 (ns/day) (hour/ns) Performance: 13.796 1.740 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (267 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.068 0.034 198.0 (ns/day) (hour/ns) Performance: 42.845 0.560 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.053 0.027 197.4 (ns/day) (hour/ns) Performance: 28.912 0.830 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.104 0.052 198.4 (ns/day) (hour/ns) Performance: 14.843 1.617 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (216 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.161 0.080 199.9 (ns/day) (hour/ns) Performance: 18.259 1.314 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.144 0.072 199.9 (ns/day) (hour/ns) Performance: 10.759 2.231 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.129 0.065 199.8 (ns/day) (hour/ns) Performance: 12.047 1.992 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (301 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.091 0.046 199.9 (ns/day) (hour/ns) Performance: 32.115 0.747 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.085 0.043 199.8 (ns/day) (hour/ns) Performance: 18.277 1.313 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.123 0.062 199.8 (ns/day) (hour/ns) Performance: 12.611 1.903 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (252 ms) [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.125 0.063 199.9 (ns/day) (hour/ns) Performance: 23.415 1.025 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.152 0.076 199.9 (ns/day) (hour/ns) Performance: 10.225 2.347 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.157 0.079 199.8 (ns/day) (hour/ns) Performance: 9.882 2.429 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NVT_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 ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (330 ms) [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (1599 ms total) [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 33.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 33.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.062 0.031 197.5 (ns/day) (hour/ns) Performance: 46.667 0.514 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.050 0.025 197.5 (ns/day) (hour/ns) Performance: 30.783 0.780 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.125 0.063 198.8 (ns/day) (hour/ns) Performance: 12.401 1.935 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (235 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.092 0.046 198.4 (ns/day) (hour/ns) Performance: 31.785 0.755 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.101 0.051 198.6 (ns/day) (hour/ns) Performance: 15.268 1.572 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.100 0.050 198.7 (ns/day) (hour/ns) Performance: 15.500 1.548 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (229 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_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 33.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_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 33.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size There were 3 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.105 0.052 199.9 (ns/day) (hour/ns) Performance: 28.054 0.856 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.069 0.035 199.8 (ns/day) (hour/ns) Performance: 22.414 1.071 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.102 0.051 199.8 (ns/day) (hour/ns) Performance: 15.217 1.577 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (228 ms) [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.139 0.069 199.9 (ns/day) (hour/ns) Performance: 21.152 1.135 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.119 0.060 199.9 (ns/day) (hour/ns) Performance: 13.025 1.843 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.097 0.048 199.8 (ns/day) (hour/ns) Performance: 16.050 1.495 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPH_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 ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (261 ms) [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (956 ms total) [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.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. WARNING 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 33.00 There were 2 notes There were 2 warnings NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.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. WARNING 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 33.00 There were 2 notes There were 2 warnings Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.066 0.033 197.9 (ns/day) (hour/ns) Performance: 44.223 0.543 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.053 0.027 196.9 (ns/day) (hour/ns) Performance: 29.075 0.825 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.105 0.053 198.6 (ns/day) (hour/ns) Performance: 14.696 1.633 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (238 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.108 0.054 198.6 (ns/day) (hour/ns) Performance: 27.096 0.886 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.094 0.048 198.3 (ns/day) (hour/ns) Performance: 16.332 1.470 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.154 0.077 198.9 (ns/day) (hour/ns) Performance: 10.065 2.385 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (275 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.064 0.033 197.7 (ns/day) (hour/ns) Performance: 45.027 0.533 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.051 0.026 196.9 (ns/day) (hour/ns) Performance: 30.294 0.792 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.125 0.063 198.6 (ns/day) (hour/ns) Performance: 12.331 1.946 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (243 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.111 0.056 198.5 (ns/day) (hour/ns) Performance: 26.206 0.916 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.124 0.062 198.7 (ns/day) (hour/ns) Performance: 12.480 1.923 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.119 0.060 198.6 (ns/day) (hour/ns) Performance: 13.007 1.845 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (269 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.061 0.031 197.0 (ns/day) (hour/ns) Performance: 47.491 0.505 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.046 0.023 196.4 (ns/day) (hour/ns) Performance: 33.219 0.722 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.060 0.030 197.4 (ns/day) (hour/ns) Performance: 25.742 0.932 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (207 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.116 0.058 198.5 (ns/day) (hour/ns) Performance: 25.153 0.954 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.104 0.053 198.4 (ns/day) (hour/ns) Performance: 14.789 1.623 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.094 0.047 198.2 (ns/day) (hour/ns) Performance: 16.466 1.458 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (243 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_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 33.00 There were 3 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_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 33.00 There were 3 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.064 0.032 197.8 (ns/day) (hour/ns) Performance: 45.691 0.525 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.088 0.045 198.1 (ns/day) (hour/ns) Performance: 17.461 1.375 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.088 0.045 198.3 (ns/day) (hour/ns) Performance: 17.461 1.374 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (219 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.122 0.061 198.9 (ns/day) (hour/ns) Performance: 23.944 1.002 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.119 0.060 198.7 (ns/day) (hour/ns) Performance: 13.016 1.844 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.164 0.083 199.0 (ns/day) (hour/ns) Performance: 9.421 2.547 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (289 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Number of degrees of freedom in T-Coupling group System is 33.00 There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.132 0.067 198.7 (ns/day) (hour/ns) Performance: 22.055 1.088 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.070 0.035 197.7 (ns/day) (hour/ns) Performance: 22.058 1.088 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.110 0.055 198.5 (ns/day) (hour/ns) Performance: 14.039 1.709 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (281 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.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. WARNING 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There were 2 warnings NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.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. WARNING 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There were 2 warnings Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.151 0.076 199.9 (ns/day) (hour/ns) Performance: 19.429 1.235 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.221 0.110 199.9 (ns/day) (hour/ns) Performance: 7.048 3.405 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.150 0.075 199.9 (ns/day) (hour/ns) Performance: 10.337 2.322 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (351 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.147 0.073 199.9 (ns/day) (hour/ns) Performance: 20.035 1.198 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.084 0.042 199.8 (ns/day) (hour/ns) Performance: 18.440 1.302 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.147 0.073 199.8 (ns/day) (hour/ns) Performance: 10.587 2.267 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (290 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.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. Number of degrees of freedom in T-Coupling group System is 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.147 0.074 199.9 (ns/day) (hour/ns) Performance: 19.949 1.203 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.138 0.069 199.9 (ns/day) (hour/ns) Performance: 11.302 2.124 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.107 0.053 199.8 (ns/day) (hour/ns) Performance: 14.552 1.649 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (281 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_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 33.00 There were 2 notes There was 1 warning NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) WARNING 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_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 33.00 There were 2 notes There was 1 warning Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.127 0.064 199.9 (ns/day) (hour/ns) Performance: 23.118 1.038 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.135 0.067 199.9 (ns/day) (hour/ns) Performance: 11.524 2.083 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.057 0.029 199.6 (ns/day) (hour/ns) Performance: 27.005 0.889 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (257 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.139 0.069 199.9 (ns/day) (hour/ns) Performance: 21.199 1.132 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.119 0.060 199.9 (ns/day) (hour/ns) Performance: 13.020 1.843 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.116 0.058 199.8 (ns/day) (hour/ns) Performance: 13.383 1.793 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (269 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 1.013 0.506 200.0 (ns/day) (hour/ns) Performance: 2.900 8.274 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.134 0.067 199.9 (ns/day) (hour/ns) Performance: 11.585 2.072 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.135 0.067 199.8 (ns/day) (hour/ns) Performance: 11.538 2.080 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (744 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (1 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (1 ms) [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.290 0.145 200.0 (ns/day) (hour/ns) Performance: 10.123 2.371 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.136 0.068 199.9 (ns/day) (hour/ns) Performance: 11.459 2.094 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.134 0.067 199.8 (ns/day) (hour/ns) Performance: 11.564 2.075 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_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 ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (369 ms) [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (4835 ms total) [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_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 There were 2 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_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 There were 2 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.117 0.058 199.9 (ns/day) (hour/ns) Performance: 25.111 0.956 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Argon' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.084 0.042 199.8 (ns/day) (hour/ns) Performance: 18.444 1.301 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.126 0.063 199.8 (ns/day) (hour/ns) Performance: 12.325 1.947 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/MTTK_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 ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (259 ms) [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (259 ms total) [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 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 1.112 nm 1.000 nm There were 3 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 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 1.112 nm 1.000 nm There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 0.848 nm, buffer size 0.148 nm Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 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 0.848 nm, buffer size 0.148 nm Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 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: 0.980 0.491 199.7 (ns/day) (hour/ns) Performance: 2.993 8.019 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.175 0.088 198.3 (ns/day) (hour/ns) Performance: 8.827 2.719 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.166 0.084 198.3 (ns/day) (hour/ns) Performance: 9.288 2.584 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (762 ms) [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 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 1.112 nm 1.000 nm There were 3 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'FirstWaterMolecule' has 3 atoms Pull group 2 'SecondWaterMolecule' has 3 atoms Number of degrees of freedom in T-Coupling group System is 9.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 2573.591 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 1.112 nm 1.000 nm There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 0.848 nm, buffer size 0.148 nm Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 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 0.848 nm, buffer size 0.148 nm Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 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: 0.172 0.086 199.2 (ns/day) (hour/ns) Performance: 16.992 1.412 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc2' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.143 0.072 199.1 (ns/day) (hour/ns) Performance: 10.817 2.219 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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: 0.176 0.088 199.2 (ns/day) (hour/ns) Performance: 8.794 2.729 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Pull_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 ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (366 ms) [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (1128 ms total) [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 Setting the AWH bias MC random seed to 2098708335 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 notes Setting the AWH bias MC random seed to -1669341187 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_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 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 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 'ALANINEDIPEPTIDE' turning H bonds into constraints... 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 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... 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.172 0.088 196.8 (ns/day) (hour/ns) Performance: 16.759 1.432 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.195 0.098 198.6 (ns/day) (hour/ns) Performance: 7.903 3.037 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.214 0.108 198.6 (ns/day) (hour/ns) Performance: 7.208 3.329 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (416 ms) [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 Setting the AWH bias MC random seed to -1417693189 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_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 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 notes Setting the AWH bias MC random seed to 985595881 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generating 1-4 interactions: fudge = 0.5 Pull group 1 'C_&_r_1' has 1 atoms Pull group 2 'N_&_r_2' has 1 atoms Pull group 3 'CA' has 1 atoms Pull group 4 'C_&_r_2' has 1 atoms Pull group 5 'N_&_r_3' has 1 atoms Number of degrees of freedom in T-Coupling group System is 51.00 NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_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 1 0 2 1 0 179.098 deg 0.000 deg 2 1 0 3 1 0 158.667 deg 0.000 deg There were 3 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 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 'ALANINEDIPEPTIDE' turning H bonds into constraints... 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 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... 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.856 0.429 199.7 (ns/day) (hour/ns) Performance: 3.427 7.003 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.166 0.084 198.2 (ns/day) (hour/ns) Performance: 9.293 2.583 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'Alanine-dipeptide' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.200 0.101 198.3 (ns/day) (hour/ns) Performance: 7.709 3.113 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Awh_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 ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (748 ms) [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1165 ms total) [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_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. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_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 2 notes NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_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. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_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 2 notes Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. 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 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 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 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 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 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 Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.211 0.106 199.9 (ns/day) (hour/ns) Performance: 13.909 1.726 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 8 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.308 0.154 199.9 (ns/day) (hour/ns) Performance: 5.042 4.760 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5 (single precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun '30 system in water' 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.290 0.145 199.9 (ns/day) (hour/ns) Performance: 5.364 4.474 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_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 ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (535 ms) [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (535 ms total) [----------] 3 tests from Checking/InitialConstraintsTest [ RUN ] Checking/InitialConstraintsTest.Works/0 Number of degrees of freedom in T-Coupling group rest is 11.00 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -680067073 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 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: 0.067 0.034 198.4 (ns/day) (hour/ns) Performance: 5.123 4.685 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (68 ms) [ RUN ] Checking/InitialConstraintsTest.Works/1 Number of degrees of freedom in T-Coupling group rest is 11.00 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -55706124 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 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: 0.060 0.030 199.8 (ns/day) (hour/ns) Performance: 5.731 4.188 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (81 ms) [ RUN ] Checking/InitialConstraintsTest.Works/2 NOTE 1 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: Integrator method md-vv-avek is implemented primarily for validation purposes; for molecular dynamics, you should probably be using md or md-vv Number of degrees of freedom in T-Coupling group rest is 11.00 NOTE 2 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: NVE simulation: will use the initial temperature of 1141.954 K for determining the Verlet buffer size NOTE 3 [file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_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 Reading file /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2022.5 (single precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI thread Using 2 OpenMP threads NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled. starting mdrun 'spc-and-methanol' 1 steps, 0.0 ps. Setting the LD random seed to -5911179 Generated 8 of the 10 non-bonded parameter combinations Excluding 2 bonded neighbours molecule type 'Methanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 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: 0.092 0.046 198.8 (ns/day) (hour/ns) Performance: 3.730 6.434 Opened /userhome/braden/software/gromacs-2022.5/buil/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (82 ms) [----------] 3 tests from Checking/InitialConstraintsTest (232 ms total) [----------] Global test environment tear-down [==========] 66 tests from 13 test suites ran. (17616 ms total) [ PASSED ] 64 tests. [ FAILED ] 2 tests, listed below: [ FAILED ] MdrunTerminationTest.CheckpointRestartAppendsByDefault [ FAILED ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 2 FAILED TESTS 0% tests passed, 1 tests failed out of 1 Label Time Summary: GTest = 17.64 sec*proc (1 test) IntegrationTest = 17.64 sec*proc (1 test) Total Test time (real) = 17.78 sec The following tests FAILED: 62 - MdrunIOTests (Failed) Errors while running CTest