[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 A. Lemkul, Ph.D.
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


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