[gmx-users] Energy profile of a single water molecule on Ni surface

[Justin Lemkul]

On 1/23/16 9:16 AM, Alexander Alexander wrote:
> Dear Gromacs user,
>
> I am a new user trying to produce the energy profile of a single water
> molecule on Ni(111) surface, I mean adsorption energy of water molecule on
> surface VS the distance of the molecule to surface. The goal is to compare
> such a profile with the same profile out of DFT.
>
> Adsorption energy in DFT is defined as:
>   {Ad_energy = [Total energy_(water-surface)] -  [Total energy_(surface)] -
> [Total energy_(water)]}
>
> How can I calculate the adsorption energy in MD - gromacs? Which one I
> should choose out of "gmx energy -f case.edr ....?  "Total-Energy" or
> "LJ-(SR)" or Potential energy ... .
>
> After lots of effort navigating the gromacs manual I could manage the
> attached inputs file for my calculations, but to be honest,  I really don't
> know how my results are reliable. So, to improve my input files and comment
> and suggestion are highly welcome.
>

The mailing list does not accept attachments.  Obtaining what you want is easy:

energygrps = surface water

in the .mdp file will do it.  Whether or not that's anywhere close to the DFT 
result depends on the force field and how it was parametrized.

-Justin

-- 
==================================================

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

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