GROMACS: gmx mdrun, version 2019.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/avp-01/Documents/tre/gromac/Mpro/Apigetrin
Command line:
gmx mdrun -v -deffnm nvt
Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 2019.4 (single precision)
Changing nstlist from 40 to 100, rlist from 1.472 to 1.532
Using 1 MPI thread
Using 16 OpenMP threads
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PME tasks will do all aspects on the GPU
Back Off! I just backed up nvt.xtc to ./#nvt.xtc.1#
Back Off! I just backed up nvt.trr to ./#nvt.trr.1#
Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
starting mdrun 'Protein in water'
125000 steps, 250.0 ps.
step 99: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
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Program: gmx mdrun, version 2019.4
Source file: src/gromacs/mdlib/sim_util.cpp (line 752)
Fatal error:
Step 100: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are 127675 and -1.08781e+06,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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