[gmx-users] surprising: what's the reason?

[Tsjerk Wassenaar]

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" <chetanvm10 at 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.abraham at 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 <chetanvm10 at 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 <tsjerkw at 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" <chetanvm10 at 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_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-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-usersor
> > > > 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.
>