[gmx-users] calculation of self energy of protein

[Saumyak Mukherjee]

Dear Justin,

Is there any way to get just the interaction energy between protein and
water? In this case, the energy should not contain the self or inherent
energy.

Thanks & regards,
Saumyak

On 27 March 2017 at 11:27, Saumyak Mukherjee <mukherjee.saumyak50 at gmail.com>
wrote:

> 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
> ================================
>
>
>


-- 
================================
*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
================================