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

Justin Lemkul jalemkul at vt.edu
Wed May 31 02:10:03 CEST 2017

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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