[gmx-users] domain decomposition Error

[Mark Abraham]

Hi,

Exactly. NVT not exploding doesn't mean it's ready for NpT, particularly if
the volume is just wrong, or you try to use parrinello rahaman too soon.

Mark

On Tue, 7 Mar 2017 09:01 MRINAL ARANDHARA <arandharamrinal at iitkgp.ac.in>
wrote:

> 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
>
> Hi,
>
> 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.
>
> Mark
>
> 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
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> >
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