[gmx-users] domain decomposition Error

[MRINAL ARANDHARA]

Hello Mark,

should I increase the NVT steps or switch to berendsen for the NPT simulation

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


----- 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??
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> >
> > --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
> > New Delhi 110025
> > India
> >
> > E-mail Id : shwetaasingh7 at gmail.com
> > Alternate e-mail id :  shweta.kumari at igib.in / shwetabis at cub.ac.in
> > Mobile No. 8409033301
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.