[gmx-users] All-atom MD simulation of a protein at 323K and 283K

[Justin Lemkul]

On 5/8/14, 2:48 AM, Pappu Kumar wrote:
> I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation in gromacs with Amber99sb in these temperature since force field parameterization was carried out in room temperature.
>
> I am also thinking about running simulated annealing from 323K to 283K in order to compare the stability of the two proteins. Thank you.
>

Such a narrow temperature range shouldn't present a problem.  People do far 
harsher things that work out fine.

-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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