[gmx-users] Free energy calculation for aminoacids

[Justin Lemkul]

On 6/27/15 8:48 AM, Marzieh Saeedi Masineh wrote:
> Hi all
> I want to calculate free energy of solvation  for a leucine and some other aminoacids individually,according to Justin tutorial : methane in the water.
> Is it reasonable to follow that  method  for free energy determination of one amino acid?
>

Yes, provided you also do the charge transformation.  The methane example is 
clearly defined as a van der Waals transformation; that is not a full hydration 
free energy.

-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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