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

Justin Lemkul jalemkul at vt.edu
Sat Oct 18 12:49:00 CEST 2014

On 10/18/14 6:45 AM, James Lord wrote:
> Dear Justin & Diogo,
> Thanks for your comments, I did the steps you guys mentioned to calculate
> protein-suface interaction energy and expect to see "protein surface"
> option upon running g_energy but it is not the case, any comments? Here is
> what I did,
> gedit md.mdp and then added at the end of md.mdp file
> energygrps= protein surface
> saved it and
> grompp -f md.mdp -c  mdw.gro -t mdw.cpt -p toplgy.top -o mdnew
> mdrun -s mdnew.tpr -rerun mdw.xtc
> g_energy -f mdnew.edr -o energy.xvg

You will not see a single energy term; rather you will see both LJ and Coulombic 
terms like LJ-SR(Protein:Surface).



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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