[gmx-users] Simulation runs indefinitely

[anu chandra]

Many thanks for the reply. I just created tpr file once again to see the
output message. But, it looks like convert-tpr showing something different
from it suppose to write about the steps. The only difference in the
previous run was that it carried out with single GPU node.

*******************************************************************************************************
GROMACS:      gmx convert-tpr, VERSION 5.0.5
Executable:   /usr/local/Cluster-Apps/gromacs/impi/5.0.5/bin/gmx_mpi
Library dir:  /usr/local/Cluster-Apps/gromacs/impi/5.0.5/share/gromacs/top
Command line:
  gmx_mpi convert-tpr -s 18md.tpr -f 18md.cpt -e 18md.edr -o 19md.tpr
-extend 20000

Reading toplogy and stuff from 18md.tpr
Reading file 18md.tpr, VERSION 5.0.5 (single precision)

NOTE: Reading the state from trajectory is an obsolete feature of gmx
convert-tpr.
      Continuation should be done by loading a checkpoint file with mdrun
-cpi
      This guarantees that all state variables are transferred.
      gmx convert-tpr is now only useful for increasing nsteps,
      but even that can often be avoided by using mdrun -maxh

NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
gmx convert-tpr can not provide binary identical continuation.
If you want that, supply a checkpoint file to mdrun


READING STATE FROM CHECKPOINT 18md.cpt...

Extending remaining runtime of by 20000 ps (now 17529120 steps)
Writing statusfile with starting step  138970880 and length   17529120
steps...
                                 time 277941.760 and length  *35058.240 ps*

gcq#333: "History has expired" (PubMed Central)
***************************************************************************************************

It written *35058.240 ps *instead of *20000ps. *I usually use mdrun as '
-cpi 18md.cpt -deffnm 19md '


Many thanks
Anu

On Wed, Jan 27, 2016 at 12:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> As suggestion suggests, you probably didn't do what you think you did,
> particularly with restarting from the checkpoint. Do a diff on your log
> files to see what was different.
>
> Mark
>
> On Wed, Jan 27, 2016 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/27/16 6:28 AM, anu chandra wrote:
> > > Hello Gromcas users,
> > >
> > > I having been simulating few membrane-protein systems for about ~300ns,
> > > using a 20 ns window for each run. Though I used the command ' gmx_mpi
> > > convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr -extend
> > 20000 '
> > > to generate the tpr file for the next run, interestingly, one of the
> > system
> > > ran for ~26000 ps and only got terminates once the run reached
> wall-clock
> > > time. All other systems terminates after successfully completing 20000
> > ps,
> > > as prescribed.  I just wonder why simulation of one of the system
> > continued
> > > indefinitely, as rest of the systems behaved as expected. All systems
> > have
> > > almost same composition, just differ in the ion concentration.
> > >
> >
> > There must be some problem in your script when you're creating the input.
> > mdrun
> > doesn't decide to run any number of steps it likes.  Probably you've
> > failed to
> > supply a checkpoint file, so the run starts over from the beginning in
> that
> > instance.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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