[gmx-users] calculation of self energy of protein

Justin Lemkul jalemkul at vt.edu
Sun Mar 26 22:52:10 CEST 2017

On 3/26/17 4:49 PM, Saumyak Mukherjee wrote:
> Dear Justin,
> Thanks for the reply.
> I have tried that already. I stripped out the protein trajectory using
> trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS
> 4.5.6), and recalculated energy using mdrun -rerun.
> But does the resulting .edr file include only the inherent energy of the
> protein or does it have information of the interaction energies with the
> solvent as well? That precisely is the point I am confused about.
> I tried this with a protein in water system and also simulated a dry
> protein separately to compare. The energies were way to different from each
> other. Does it mean that the solvent-protein interaction energies are also
> involved?

If you have a protein-only trajectory and a protein-only .tpr file, there's no 
possible way for there to be any sort of protein-solvent interaction energy. 
The energies of a "wet" and "dry" protein system should be extremely different.



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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