[gmx-users] Simulation runs indefinitely

[Justin Lemkul]

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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