[gmx-users] energy

[Justin Lemkul]

On 5/9/14, 9:38 AM, mirko busato wrote:
> Dear Justin,
>
> Thank you very much for your quick reply,
>
> In my .mdp file I set up energygrps to protein ITA.
> (ITA is the group for the Itaconic acid monomers)
>
> After that I tried to launch g_energy command on .edr file.
>
> Is it right?
>
> which energy terms do you suggest me to use for my problem (to understand the
> affinity peptide-monomer)?
>

The short-range nonbonded terms are the only ones that get decomposed in a 
pairwise fashion, so the new terms should be fairly obvious from the screen output.

Whether or not those numbers mean anything is another story; they may give you 
some insight into the enthalpic driving forces, but they tell you nothing of the 
actual free energy of binding.

-Justin

-- 
==================================================

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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