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

[Saumyak Mukherjee]

Thanks a lot for your comments.

I am doing the calculations using a self-written FORTRAN code.

On 31 May 2017 at 17:23, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/31/17 12:24 AM, Saumyak Mukherjee wrote:
>
>> 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?
>>
>>
> That *is* possible with energygrps but you'll have to do each calculation
> separately using different groups.  Very tedious.
>
> -Justin
>
>
> 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
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
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>>> University of Maryland, Baltimore
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>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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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
>
> ==================================================
> --
> Gromacs Users mailing list
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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
================================