[gmx-users] confusion on energy for a system of protein sovated in water
jalemkul at vt.edu
Tue Feb 23 15:54:24 CET 2016
On 2/22/16 10:03 PM, Ming Tang wrote:
> Thanks Justin,
> How about LJ and Coulomb energy?
> I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb force within the protein only?
The "protein energy" usually tells you nothing. Unless you're doing a more
rigorous calculation like MM/PBSA, I wouldn't try to base anything off of these
quantities. They're not free energies and they're totally force field-dependent
results. From your previous post, I'm assuming you're using GROMOS96, which,
while parametrized against free energies of solvation, does not guarantee that
such short-range interaction energies actually correspond to something
physically useful (unlike, e.g. CHARMM, which is directly parametrized against
QM water interaction energies).
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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