[gmx-users] drug-drug interaction energy

[Justin Lemkul]

On 4/2/14, 12:23 PM, Manuel Azenha wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the
> self-aggregation, and try to determine the interaction energy between the
> drug molecules , I'm getting net positive values whatever the drug. I'm
> simply defining the drug groups in .mdp. Should it be entered some other way
> ?

How do those energies compare to the drug-water or drug-methanol energies? 
Remember that a pairwise nonbonded interaction energy is not a free energy.  If 
you used PME, the value returned by energygrps isn't even fully accurate because 
the mesh term is not decomposed.  The magnitude of the effect probably depends 
on the size of the molecules being considered and the distance over which they 
interact.

-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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