I referred to the manual, and there seems to be no detail information about
how to continue from a crashed run. For example, I want to do 10ns MD
simulation, but the walltime limit forced my job to stop at 2.5ns.
I understand that I should use the restrt file from the point 2.5ns, but
should I rewrite the .mdin file to decrease the total simulation time to
7.5ns? Or I can just use the original .mdin file?
Thanks,
Yun
On Wed, Aug 17, 2011 at 10:40 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Use the restart file from the previous simulation to start your next
> simulation. If you are restarting a simulation, you'll have to set the ntx
> variable to 5 in the mdin file and the irest variable to 1.
>
> See the Amber manual for details.
>
> HTH,
> Jason
>
> On Wed, Aug 17, 2011 at 12:03 PM, Yun Shi <yunshi09.gmail.com> wrote:
>
> > Hi all,
> >
> > There is a walltime limit on the clusters I am using, which means I
> cannot
> > finish a 10ns or 100ns MD simulation within the time limit.
> >
> > How could I terminate my MD job gracefully within 24 hours? In other
> words,
> > what should I do to continue from the previous part of simulation?
> >
> > Any help is appreciated!
> >
> > Yun Shi
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 17 2011 - 11:00:07 PDT
