Hi Mark, Could you clarify what is meant by "gentle" and why does it help solve the issue?
Thanks Chetan On Sun, Mar 16, 2014 at 8:29 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Ja. Rebuilding the neighbor list more often is more gentle, which often > helps. The output period has nothing directly to do with it. > > Mark > On Mar 16, 2014 8:18 AM, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: > > > Hi Chetan, > > > > nstenergy = 1 requires nstcalcenergy = 1, which requires nstlist = 1. You > > might want to try setting only the latter, and check nstpcoupl. > > > > Hope it helps , > > > > Tsjerk > > On Mar 16, 2014 7:17 AM, "Chetan Mahajan" <chetanv...@gmail.com> wrote: > > > > > Hi Mark, Tsjerk and others interested, > > > > > > I changed the frequency of nstxout, nstvout, nstlog, nstenergy, > nstxtcout > > > in equilibration run from 1000 to 1 and Whoa! the entire code (even if > > the > > > frequency of these in production run is still 1000) is running fine > now. > > > That box vector error is gone. I wonder what's going on, but I am happy > > > code is working. I have confirmed this by reproducing this run yet > again. > > > ( Code still gives box vector error when output frequency is 1000 > > instead > > > of 1 ). > > > > > > Thanks > > > Chetan > > > > > > > > > On Wed, Mar 12, 2014 at 4:20 AM, Mark Abraham < > mark.j.abra...@gmail.com > > > >wrote: > > > > > > > Sounds like a normal case of being too rough with a system during > > > > equilibration, which can lead to > > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up if you > get > > > > unlucky. There's general advice there. > > > > > > > > Mark > > > > > > > > > > > > On Wed, Mar 12, 2014 at 7:05 AM, Chetan Mahajan < > chetanv...@gmail.com > > > > >wrote: > > > > > > > > > Hi Tsjerk, > > > > > > > > > > Thanks. It is on the same machine Stampede, same number of nodes > and > > > > > processors. It does go through minimization part (5000 steps) well > > and > > > > > gives this error near the start of equilibration run, which comes > > after > > > > > minimization. > > > > > > > > > > Thank you. > > > > > > > > > > regards > > > > > Chetan > > > > > > > > > > > > > > > On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar < > > tsje...@gmail.com > > > > > >wrote: > > > > > > > > > > > Hi Chetan, > > > > > > > > > > > > Was it on the same machine/node(s)? Same number of processors? > How > > > many > > > > > > steps until the error? Any difference may cause a different > > outcome. > > > > > > > > > > > > Cheers, > > > > > > > > > > > > Tsjerk > > > > > > On Mar 12, 2014 5:42 AM, "Chetan Mahajan" <chetanv...@gmail.com> > > > > wrote: > > > > > > > > > > > > > Hi > > > > > > > > > > > > > > I am testing one MD run using gromacs. 2 days back it ran fine. > > > Today > > > > > > when > > > > > > > I ran the "exactly same" code again, it gave following error: > > > > > > > > > > > > > > > > > > > > > Increasing the number of cell to communicate in dimension X to > 3 > > > for > > > > > the > > > > > > > first time > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > > > Program mdrun_mpi, VERSION 4.6.3 > > > > > > > Source code file: > > > > > > > > > > /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c, > > > > > > line: > > > > > > > 2730 > > > > > > > > > > > > > > Fatal error: > > > > > > > One of the box vectors has become shorter than twice the > cut-off > > > > length > > > > > > or > > > > > > > box_yy-|box_zy| or box_zz has become smaller than the cut-off. > > > > > > > > > > > > > > I am confused as to why same run should give different answers > on > > > > > > different > > > > > > > occasions. Is it pointing to something wrong with the gromacs > > > > > executable > > > > > > I > > > > > > > have or something else? > > > > > > > > > > > > > > Thank you. > > > > > > > > > > > > > > regards > > > > > > > Chetan > > > > > > > -- > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore > > > > > > > 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-usersor > > > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore > > > > > > 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-usersor > > > > > > send a mail to gmx-users-requ...@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-usersor > > > > > send a mail to gmx-users-requ...@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-usersor > > > > send a mail to gmx-users-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.