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
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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
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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)
Hi, the error suggested the solution as well. It is likely due to your poor starting structure. Check these "8443 and 8444" atoms in your PDB (or gro file, may be the number differs between the two files, so better check the gro), how they look and how far they are with respect to other atoms. I hope you will get the answer.
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