[gmx-users] Domain decomposition error

[Justin Lemkul]

On 5/18/17 5:59 AM, Kashif wrote:
> I got this error every time when I try to simulate one of my protein-ligand
> complex.
>
>  -------------------------------------------------------
> 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.
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================