[gmx-users] calculation of energy of individual water molecules in gromacs
mukherjee.saumyak50 at gmail.com
Wed May 31 06:25:10 CEST 2017
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 A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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