[gmx-users] calculation of energy of individual water molecules in gromacs
jalemkul at vt.edu
Wed May 31 13:53:33 CEST 2017
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.
> 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
>> 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
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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
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