[gmx-users] Simulation runs indefinitely

[Mark Abraham]

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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