[gmx-users] Interaction energy between helices

[Justin Lemkul]

On 6/11/14, 5:36 PM, Natalia Alveal F. wrote:
> Dear Gromacs users,
> I want to calculate the energy of interaction between two helices of a
> protein, but g_energy dont have the option for -ndx file to select these
> specific residues of a helix. How I can do this?
>

That's what energygrps in the .mdp file are for.  Re-calculate the energies with 
mdrun -rerun using the new .tpr file.

-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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