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

[VITALY V. CHABAN]

On Sat, Jan 23, 2016 at 12:16 PM, Alexander Alexander <
alexanderwien2k at gmail.com> 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.
>
>


I would do that using some of global optimization algorithms. MD will not
give you a profile.

Steered MD is an option, as well.

Here is the example: http://vixra.org/pdf/1512.0290v1.pdf





> 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 ... .
>
>


You need to sum up all components relating to potential energy, like LJ,
Coulomb, PME-Coulomb part, and so on

This is to be done for every species separately and together to insert into
the above formula.







> 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.
>
> Thank you so much in advance.
>
> Cheers,
>
> Alex
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>