[gmx-users] calculating interaction energies of dimers and ligand

Justin Lemkul jalemkul at vt.edu
Fri Feb 13 15:46:24 CET 2015

On 2/13/15 7:07 AM, RJ wrote:
> Dear all,
> I need to calculate the interaction energy (Column SR & LJ SR) of chain A with chain B.
> Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so?

To get this information printed to the .edr file, you need to do your run with 
correct energygrps defined.  If you didn't do that, create a .tpr file that 
specifies these groups and re-calculate energies with mdrun -rerun.

> Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)?

Just convert after the fact in the text file or plotting software.  The time 
unit is always ps in .edr files.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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