[gmx-users] calculation of self energy of protein

[Justin Lemkul]

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

==================================================