[gmx-users] Equilibration fails only when run from script

R Corey R.Corey at bristol.ac.uk
Tue Dec 1 12:40:03 CET 2015


I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as below:

Fatal error:
3 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

However, the weird thing is that if I re-run the script the next day,
choosing only failed jobs to rerun, some of them now work fine. And if I
simply mdrun each tpr from the command line it runs fine too.

Is this expected, that a tpr file for an NVT equilibration will crash one
day but run fine the next?



*Robin Corey*
PhD Student
School of Biochemistry
University of Bristol
University Walk
Bristol BS8 1TD
r.corey at bristol.ac.uk

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