GROMACS version:2021
GROMACS modification: No
Here post your question :gmx mdrun -deffnm nvt
:-) GROMACS - gmx mdrun, 2021.4-Ubuntu-2021.4-2 (-:
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GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/parul/umb_samp_iiserprac/au_lig_atp
Command line:
gmx mdrun -deffnm nvt
Back Off! I just backed up nvt.log to ./#nvt.log.1#
Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see
log).
Reading file nvt.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Changing nstlist from 10 to 80, rlist from 1 to 1.096
Using 1 MPI thread
Using 8 OpenMP threads
Back Off! I just backed up nvt.trr to ./#nvt.trr.1#
Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
WARNING: This run will generate roughly 3336 Mb of data
starting mdrun ‘128-Lipid DPPC Bilayer in water’
50000 steps, 50.0 ps.
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 21.651808, max 75.004066 (between atoms 8443 and 8444)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
8443 8444 90.0 0.1010 7.6764 0.1010
Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#
Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#
Wrote pdb files with previous and current coordinates
Step 2, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 125.736237, max 435.563080 (between atoms 8443 and 8444)
bonds that rotated more than 30 degrees:
** atom 1 atom 2 angle previous, current, constraint length**
** 8443 8444 122.3 7.6764 44.0929 0.1010**
step 2: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step2b.pdb to ./#step2b.pdb.1#
Back Off! I just backed up step2c.pdb to ./#step2c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
when i am trying to do the md run of my system for Equilibration(NVT), I am getting this error, I had TRued to minimise my time step But still error is persisting < I had Tried to add pores file also in topology ,same error persist ,Please Guide me .