[gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite

zeineb SI CHAIB zeineb-14 at hotmail.com
Tue Feb 26 10:57:42 CET 2019

Dear Kevin,

Thank you for your reply.

I did 2 tests:
1- I wanted to see in details when the system crashes and which atoms are involved so I restarted the simulation from the checkpoint but using a new mdp file. The only parameter that I changed was nstxout-compressed  = 1. In this case, the simulation didn't crash.
The command lines that I used were:
gmx grompp -f md_2.mdp -c npt.gro -p topol.top -n index.ndx -o md_2.tpr
gmx mdrun -deffnm md_2 -cpi md.cpt -noappend -nt 1

2- I restarted the simulation from the same checkpoint as in (1), using the first mdp file (with nstxout-compressed = 1000) and the simulation crashed again at the same step.
The command line that I used were:
gmx mdrun -deffnm md -cpi md.cpt -noappend -nt 1

I compared the log files of (1) and (2) and it's starting from the same time/steps but as I said (1) didn't crash and (2) crashed.

I can restart the simulation with the new mdp file and keep it running again but I want to be sure that It's a random crash and it is not a sign of something more fundamentally wrong (physically unrealistic) with my system.


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