[gmx-users] domain decomposition Error

[Mark Abraham]

Hi,

On Tue, Mar 7, 2017 at 12:24 PM MRINAL ARANDHARA <
arandharamrinal at iitkgp.ac.in> wrote:

> Hello Mark,
>
> should I increase the NVT steps


If either of my guesses about the problem were correct, would this help?


> or switch to berendsen for the NPT simulation
>

I can't tell, because I know nothing about your volume, expected density or
NPT protocol. There's lots of resources that make suggestions for
equilibration protocols, and some of them are even linked from the errors
page I already pointed you towards. Did you explore there?


> Actually my system is very big and has around 147891 water residues and
> more than one residues with the same residue name  SOL.Hope thts not the
> problem
>

Yes, that's true for you and every other person doing explicit solvent
simulations :-)

Mark

----- Original Message -----
> From: "Mark Abraham" <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Sent: Tuesday, March 7, 2017 4:25:12 AM
> Subject: Re: [gmx-users] domain decomposition Error
>
> 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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> > > New Delhi 110025
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