[gmx-users] calculation of self energy of protein

[Saumyak Mukherjee]

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?

Thanks and regards,
Saumyak

On 26 March 2017 at 19:51, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/26/17 10:06 AM, Saumyak Mukherjee wrote:
>
>> Yes, I need to calculate the inherent potential energy of the protein.
>>
>>
> You can strip the protein coordinates from the original trajectory, create
> a matching .tpr with convert-tpr and re-calculate energies with mdrun
> -rerun.  The quantity is a force field-dependent potential energy and is
> unlikely to be useful, though.
>
> -Justin
>
>
> On 26 March 2017 at 14:33, Souparno Adhikary <souparnoa91 at gmail.com>
>> wrote:
>>
>> Do you mean the potential energy of the protein?
>>>
>>> On 26 Mar 2017 14:24, "Saumyak Mukherjee" <mukherjee.saumyak50 at gmail.com
>>> >
>>> wrote:
>>>
>>> Dear Users,
>>>>
>>>> How can the self energy of a protein be calculated from GROMACS. This
>>>>
>>> means
>>>
>>>> that I want only the inherent energy of the protein, excluding the
>>>> interaction energy with the surrounding solvent.
>>>>
>>>> Adding to this, is it possible to calculate such inherent energy of any
>>>> selected domain in the system, such as the hydration layer around
>>>>
>>> protein?
>>>
>>>>
>>>> Thanks and regards,
>>>>
>>>> ================================
>>>> *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
>>>> ================================
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>>
>>
>>
> --
> ==================================================
>
> 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
================================