[gmx-users] Fwd: Domain decomposition error
mark.j.abraham at gmail.com
Tue May 2 11:36:16 CEST 2017
If the topology works e.g. for drug in water, and you get problems with
blowing up only with the complex, then likely the starting pose is crude,
e.g. gaps with missing solvent, or overlapping atoms. Use a visualization
program and look carefully. The standard advice here applies:
On Sat, Apr 29, 2017 at 12:43 PM Kashif <kashifzamir180.mk at gmail.com> wrote:
> ---------- Forwarded message ----------
> From: <gromacs.org_gmx-users-owner at maillist.sys.kth.se>
> Date: Sat, Apr 29, 2017 at 3:02 PM
> Subject: Re: Domain decomposition error
> To: kashifzamir180.mk at gmail.com
> I got this error every time when I try to simulate one of my protein-ligand
> Program mdrun, VERSION 4.6.6
> Source code file: /root/Documents/gromacs-4.6.6/src/mdlib/pme.c, line: 851
> Fatal error:
> 1 particles communicated to PME node 5 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.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Although, same parameters in mdp files fairly simulated the other
> drug-protein complex. But this drug complex is creating trouble.
> kindly help.
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