On Nov 28, 2011, at 8:56 AM, "Beale, John" <John.Beale.stlcop.edu> wrote:
>
> I am trying to run long pmemd jobs on a protein in explicit water. I am reaching the maximum time that our cluster will allow for one job, and to continue it is necessary for me to restart a second part of the simulation. I want to continue from where the simulation stopped. Let's say that my simulation had 1,000,000 steps (not the real number). I would like to continue at step 1,000,001. But, when I try to restart the system goes back to step1 instead of adding on to what was already run.
This is the only behavior available. The time, on the other hand, will continue from the last simulation. Is the time not more useful than NSTEP? They should be directly related.
NSTEP is an attribute of a single simulation, so it doesn't really make sense in that definition to have it continue from the last restart. Furthermore, there's no way to determine the step that the last simulation ended on, which makes this approach impossible unless you change the format of the restart file.
HTH,
Jason
> How can I set it up so I can just continue. I would also like to add the second-part rst and trajectory information onto what was already run. Is there a way to do this?
>
> John
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 28 2011 - 06:30:03 PST
