[gmx-users] domain decomposition Error
arandharamrinal at iitkgp.ac.in
Tue Mar 7 09:00:57 CET 2017
Thank You Mark for the reply.
The error comes during the npt equillibration step only and not during the nvt equillibration step. I have successfully done 1-ns of nvt equillibration.
--- -- Original Message -----
From: "Mark Abraham" <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Sent: Tuesday, March 7, 2017 2:32:46 AM
Subject: Re: [gmx-users] domain decomposition Error
There's good advice for this problem at think link that was suggested in
the error message: http://www.gromacs.org/Documentation/Errors. Probably
your box volume or NpT protocol need some attention.
On Tue, 7 Mar 2017 06:23 shweta singh <shwetaasingh7 at gmail.com> wrote:
> Thank you !
> On Tue, Mar 7, 2017 at 9:47 AM, MRINAL ARANDHARA <
> arandharamrinal at iitkgp.ac.in> wrote:
> > I am trying to run a lipid bilayer simulation but during the npt
> > equillibration step I am getting the following error
> > "1 particles communicated to PME rank 6 are more than 2/3 times the
> > cut-off out of the domain decomposition cell of their charge group in
> > dimension y"
> > I have successfully run the NVT equillibration.What may be the problem??
> > --
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> --Thanks and Regards--
> Shweta Kumari
> M.Sc. Bioinformatics
> Central University Of South Bihar, Patna
> Project Assistant
> Computational Structural Biology lab
> CSIR-Institute of Genomics and Integrative Biology
> Mathura Road, Sukhdev Vihar
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