[gmx-users] Can I make Free Energy Calculations for Protein and Water System?

[Justin Lemkul]

On 8/13/14, 9:05 AM, Batdorj Batsaikhan wrote:
> Dear gmx users,
>
> I want to calculate free energy calculations for protein and water system.
> There are many free energy calculation tutorials for small molecule and water
> system. I want to make free energy calculations for a protein and water
> system. How can I free energy calculations for this sistem? Can you advice
> me? Thank you
>

The process is the same.  If you're interested in binding free energy, do the 
transformation in the protein and in water and compute DGbind from the 
thermodynamic cycle.  There's a massive amount of literature on this topic, 
including excellent reviews that cover just about everything you need to know.

-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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