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

[Mark Abraham]

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
> > > --
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