[gmx-users] calculation of self energy of protein

[Saumyak Mukherjee]

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
>> 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
>
>
> --
> ==================================================
>
> 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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-- 
================================
*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukherjee at gmail.com
                                smukherjee at sscu.iisc.ernet.in
================================