[gmx-users] protein-DNA complex

[Justin Lemkul]

On 2/29/16 4:25 AM, Mahboobeh Eslami wrote:
> dear Justin
> thanks for your answer
> I have another question. Which of the following items is better in mdp file for
> the equilibration and MD production steps?
>
> tc-grps       = Protein-DNA    SOL-ION
>
> or
> tc-grps       = Protein   DNA   SOL-ION
>

Probably irrelevant if the protein and DNA are of reasonably large size.  I 
would probably couple the complex together.

-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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