[gmx-users] calculation of self energy of protein
mukherjee.saumyak50 at gmail.com
Mon Mar 27 07:58:30 CEST 2017
Thank you very much.
On 27 March 2017 at 02:22, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> other. Does it mean that the solvent-protein interaction energies are also
> 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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Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
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Alternative e-mail : saumyakmukherjee at gmail.com
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