[gmx-users] confusion on energy for a system of protein sovated in water

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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