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