[gmx-users] Gromacs 5.0.1 restart simulation

Justin Lemkul jalemkul at vt.edu
Wed Dec 3 00:30:11 CET 2014

On 12/2/14 6:22 PM, wh wrote:
> Dear Gromacs Users,
> Recently when I tried to restart a md simulation from previous one using
> convert-tpr with version 5.0.1 , the task failed giving the error message:
> X particles communicated to PME node Y are more than a cell length out of the
> domain decomposition cell of their charge group
> I tried several way to solve it, including modify the equilibration setting
> as it said in the gromacs error page, and all failed. If I just run one
> simulation for a long time, it will not crash, at least can do further than
> the time point it crashed when using restart.
> Does anyone have any idea why this happen and how to solve it?  I used the
> syntax:
> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o output.tpr -extend
> 10000
> Any suggestion will be greatly appreciated

Do not supply .trr and .edr files; just increase the number of steps and
continue from the existing checkpoint with mdrun -cpi.  What you're doing is
based on ancient syntax that is no longer relevant.  I'm guessing that you're
probably winding up with discontinuous states somehow.




Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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