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

[Chetan Mahajan]

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.abraham at 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" <tsjerkw at 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" <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
> > > > > > > --
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