:-) GROMACS - gmx grompp, 2023.1 (-: Executable: /amorphous/apps/gromacs-2023.1/bin/gmx Data prefix: /amorphous/apps/gromacs-2023.1 Working dir: ************************************************************** Command line: gmx grompp -f step6.1_equilibration.mdp -o step6.1_equilibration.tpr -c step6.0_minimization.gro -r step5_input.gro -p topol.top -n index.ndx -maxwarn 2 Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Generating 1-4 interactions: fudge = 1 Simulated annealing for group SOLU: Single, 2 timepoints Time (ps) Temperature (K) 0.0 1.0 20.0- 100.0 Simulated annealing for group MEMB: Single, 2 timepoints Time (ps) Temperature (K) 0.0 1.0 20.0- 100.0 Simulated annealing for group SOLV: Single, 2 timepoints Time (ps) Temperature (K) 0.0 1.0 20.0- 100.0 Number of degrees of freedom in T-Coupling group SOLU is 21845.61 Number of degrees of freedom in T-Coupling group MEMB is 147197.39 Number of degrees of freedom in T-Coupling group SOLV is 327888.00 Simulated tempering is used with multiple T-coupling groups: setting the ensemble temperature to not available NOTE 1 [file step6.1_equilibration.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible. WARNING 1 [file step6.1_equilibration.mdp]: With a verlet-buffer-tolerance of 0.005 kJ/mol/ps, a reference temperature of 1 and a tau_t of 1, your temperature might be off by up to 15.0%. To ensure the error is below 0.1%, decrease verlet-buffer-tolerance to 3e-05 or decrease tau_t. There was 1 NOTE There was 1 WARNING Back Off! I just backed up step6.1_equilibration.tpr to ./#step6.1_equilibration.tpr.3# GROMACS reminds you: "It Doesn't Have to Be Tip Top" (Pulp Fiction) Setting the LD random seed to -14716115 Generated 3069 of the 3081 non-bonded parameter combinations Generated 1714 of the 3081 1-4 parameter combinations Excluding 3 bonded neighbours molecule type turning H bonds into constraints... Excluding 3 bonded neighbours molecule type turning H bonds into constraints... Excluding 3 bonded neighbours molecule type turning H bonds into constraints... Excluding 3 bonded neighbours molecule type turning H bonds into constraints... Excluding 1 bonded neighbours molecule type turning H bonds into constraints... Excluding 1 bonded neighbours molecule type turning H bonds into constraints... Excluding 2 bonded neighbours molecule type turning H bonds into constraints... Setting gen_seed to -12148849 Velocities were taken from a Maxwell distribution at 1 K The largest distance between excluded atoms is 0.524 nm between atom 56 and 62 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1 K Calculated rlist for 1x1 atom pair-list as 1.200 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 112x112x128, spacing 0.116 0.116 0.115 Estimate for the relative computational load of the PME mesh part: 0.18 This run will generate roughly 154 Mb of data :-) GROMACS - gmx mdrun, 2023.1 (-: Executable: /amorphous/apps/gromacs-2023.1/bin/gmx Data prefix: /amorphous/apps/gromacs-2023.1 Working dir: *********************************************** Command line: gmx mdrun -v -deffnm step6.1_equilibration -ntmpi 8 -npme 1 -pme gpu -update cpu -nb gpu -bonded gpu Back Off! I just backed up step6.1_equilibration.log to ./#step6.1_equilibration.log.3# Reading file step6.1_equilibration.tpr, VERSION 2023.1 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms On host gx03 4 GPUs selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 8 ranks on this node: PP:0,PP:0,PP:1,PP:1,PP:2,PP:2,PP:3,PME:3 PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU Using 8 MPI threads Using 4 OpenMP threads per tMPI thread Back Off! I just backed up step6.1_equilibration.xtc to ./#step6.1_equilibration.xtc.3# Back Off! I just backed up step6.1_equilibration.trr to ./#step6.1_equilibration.trr.3# Back Off! I just backed up step6.1_equilibration.edr to ./#step6.1_equilibration.edr.3# NOTE: DLB will not turn on during the first phase of PME tuning starting mdrun 'Title' 20000 steps, 20.0 ps. ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- Program: gmx mdrun, version 2023.1 Program: gmx mdrun, version 2023.1 ------------------------------------------------------- Program: gmx mdrun, version 2023.1 Program: gmx mdrun, version 2023.1 Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: ------------------------------------------------------- Program: gmx mdrun, version 2023.1 Program: gmx mdrun, version 2023.1 Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: ------------------------------------------------------- Program: gmx mdrun, version 2023.1 Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: MPI rank: 5 (out of 8) MPI rank: 6 (out of 8) MPI rank: 1 (out of 8) MPI rank: 4 (out of 8) MPI rank: 3 (out of 8) Source file: src/gromacs/mdtypes/inputrec.cpp (line 1674) Assertion failed: Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: Function: assertValidEnsembleTemperatureSetting(EnsembleTemperatureSetting):: MPI rank: 0 (out of 8) MPI rank: 2 (out of 8) Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable Assertion failed: Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable Assertion failed: At this point in the code the ensemble temperature setting cannot be auto Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable Assertion failed: Assertion failed: At this point in the code the ensemble temperature setting cannot be auto At this point in the code the ensemble temperature setting cannot be auto Assertion failed: Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable At this point in the code the ensemble temperature setting cannot be auto For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Assertion failed: Condition: rts == EnsembleTemperatureSetting::NotAvailable || rts == EnsembleTemperatureSetting::Constant || rts == EnsembleTemperatureSetting::Variable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors