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

[Chetan Mahajan]

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
> > > > --
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