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 <[email protected]> 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" <[email protected]> > To: [email protected] > 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 <[email protected]> wrote: > > > Thank you ! > > > > On Tue, Mar 7, 2017 at 9:47 AM, MRINAL ARANDHARA < > > [email protected]> 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 [email protected]. > > > > > > > > > > > -- > > > > --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 : [email protected] > > Alternate e-mail id : [email protected] / [email protected] > > 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 [email protected]. > > > -- > 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 [email protected]. > -- > 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 [email protected]. > -- 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 [email protected].
