Re: [gmx-users] Fwd: Domain decomposition error

[Mark Abraham]

Hi,

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

Mark

On Sat, Apr 29, 2017 at 12:43 PM Kashif  wrote:

> -- Forwarded message --
> From: 
> Date: Sat, Apr 29, 2017 at 3:02 PM
> Subject: Re: Domain decomposition error
> To: kashifzamir180...@gmail.com
>
>
> 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.
>
> regards
> kashif
>
>
> 
> >
> >
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[gmx-users] Fwd: Domain decomposition error

[Kashif]

-- Forwarded message --
From: 
Date: Sat, Apr 29, 2017 at 3:02 PM
Subject: Re: Domain decomposition error
To: kashifzamir180...@gmail.com


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.

regards
kashif



>
>
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