[gmx-users] energy minimization error

[Justin Lemkul]

On 6/27/15 2:29 AM, James Lord wrote:
> Hi Justin
> For now I  used
>
>
> *mdrun -nt 1*
>
>
> * and got rid of this error so hopefully the simulation wont crash. *
>

The DD errors have nothing to do with physical stability; you just can't 
necessarily parallelize any arbitrary system over any arbitrary number of cores 
(DD cells).  You can also parallelize with OpenMP to get some speed-up (mdrun 
-ntmpi 1 -ntomp N).

-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 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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