You can use the same mdin file, setting first the ntx and irest
variables as Jason told you before, and always using the previous
restart file to run the next one. So, to run from 2,5 to 5 ns, you
have to use the restrt file generated in the first 2,5 ns of simulation.
Sergio.
> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 17 2011 - 12:00:03 PDT
