[gmx-users] How to calculate protein-surface interaction energy

Justin Lemkul jalemkul at vt.edu
Thu Oct 16 18:07:28 CEST 2014

On 10/16/14 11:42 AM, James Lord wrote:
> Hi Justin,
> Sorry for not being clear, I have done the simulation without specifying
> the energygrps, so based on your previous comment I should use mdrun -rerun
> trj.xtc -o energy.edr -pn index.ndx?  and in index file define energygrps =
> Protein Surface right?
> If not appreciate if you give an example of the command with appropriate
> input output etc.

Create a new .tpr with the .mdp file that specifies the desired energygrps, then:

mdrun -s new.tpr -rerun trj.xtc



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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