[gmx-users] producing several trajectories to check for reproducibility

[Justin Lemkul]

On 5/25/14, 7:30 AM, Saman Shahriyari wrote:
> dear users
> I am trying to have several trajectories for one simulated  system to check if my results are reproducible or not. should I be making several .tpr files with the same pdb file or is there any way I can have several random seeds for the mud run command? i mean is there any way i can do the mdrun once and have several trajectories generated?

Set a different value of gen_seed in the .mdp file (thus creating several 
distinct .tpr files) at the outset of the simulations, i.e. equilibration.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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