[gmx-users] calculation of energy of individual water molecules in gromacs

[Saumyak Mukherjee]

Thanks Justin for the reply.

Supposing that I have 2300 (average) water molecules in a 1 nm hydration
shell around a protein, I need to calculate the interaction energy of each
and everyone of them in all the time frames, with the rest of the system. I
believe this is not possible using energygrps. Is there any other way?

On 31 May 2017 at 05:39, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/30/17 1:52 AM, Saumyak Mukherjee wrote:
>
>> Dear users,
>>
>> I need to calculate the energy of individual water molecules in a 1 nm
>> shell around protein. That is, there will be n number of energy terms in
>> each time frame if there are n number of water molecules in the said
>> hydration shell at that time step. Is there a way to do it in GROMACS?
>>
>>
> The internal energy of a water molecule?  If you're using standard rigid
> waters, that quantity is by definition zero.  Interaction energy is another
> matter and can be calculated using energygrps.  Whether or not that's
> useful depends on the force field, as I just commented in another thread.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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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
================================