[gmx-users] Interaction energy between specific residue in a set of residues

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 22:27:52 CEST 2013



On 7/31/13 4:20 PM, Collins Nganou wrote:
> Dear all,
>
> I am looking how  I can extract the interaction energy between  specific
> residue in a set of  residues.
>

Nonbonded energy terms are decomposed using energygrps in the .mdp file along 
with suitable index groups.

> example:
>
> I have DT and DA residues, I would like to plot only the energy of the DT.
> I can extract the DT with the index file, But I am missing information on
> how to plot the energy base on my index file where I can select only DT.
>

You can create index groups for any base or bases you want individually.  You 
haven't shown us what you've done, so it's hard to critique beyond that.

> I was only looking the way to extract the c5-c6 distance of adjacent DT
> without include DA.
>

Distances are calculated with g_dist and suitable index groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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