> Date: Sun, 10 Mar 2013 03:17:24 -0700 (PDT) > From: Hamid Mosaddeghi <hamid5920...@yahoo.com> > Subject: [gmx-users] Re: gromacs VERSION 4.0.7-There is no domain > decomposition..... > To: gmx-users@gromacs.org > Message-ID: <1362910644976-5006251.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Dear Christoph > > thanks for quick reply > >>It seems like mdrun was not able to find a decomposition >>automatically, try to give one by hand: >>$ mdrun -dd 2 2 4 > > this command is general or not? No, it is not general, but you wanted to run on 16 cores, so a decomposition of 2x2x4 (=16 and 4 in z as the box was the longest in z) would work. > >>Btw, your gromacs is 2 major versions behind, it might be a good idea to > update > > yes, but I modify some force field in this versiom nad need to work with it If this change is of general interest, create a patch and submit it here: <https://gerrit.gromacs.org/>
> > > do you think I go to new version, don't get this error? Many many things has been improved from 4.0 to 4.6, so I think it is save to say it will most likely work. > > Best Regards > > Hamid Mosaddeghi > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Re-gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006247p5006251.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 107, Issue 42 > ****************************************** -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists