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

Kevin Boyd kevin.boyd at uconn.edu
Wed Feb 27 18:15:22 CET 2019


If it was something fundamentally wrong, you'd see an issue before this.
Martini is just inherently a teensy bit unstable - but this is where the
non-reproducibility of simulations comes in handy; restarting from far
enough away will likely avoid a transiently high energy event.


On Tue, Feb 26, 2019 at 4:57 AM zeineb SI CHAIB <zeineb-14 at hotmail.com>

> 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.
> Zeineb
> --
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