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" <[email protected]> To: [email protected] 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 <[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]. -- 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].
