[gmx-users] watrebox with osmolites

[Justin Lemkul]

On 9/30/14 3:31 PM, niyaz.sabir wrote:
> Dear Gromacs users,
> Is there any tutorial to simulate a protein in water solution containing neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of the compound on protein stability/secondary structure flexibility is to be considered.

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

Add your osmolyte with genbox (gmx insert-molecules in 5.0) -ci -nmol, update 
the topology, and solvate as usual with water.

-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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