[gmx-users] Tabulated potential for metal-oxide

[Mark Abraham]

On 28/06/2011 8:49 PM, manana koberidze wrote:
> Dear All,
>
> I've just started using GROMACS, I've read the manual and searched the 
> mailing list but still confused. I'm trying to simulate metal 
> oxidation with GROMACS. As a first step, I'm trying to tabulate the 
> EAM (Embedded atom potential), which in addition to residual pair-pair 
> repulsion includes the energy required to embed atom i in a local 
> electron density rho, where rho is defined as:
>                                 rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }
> k, beta, r*_j are known parameters and the sum runs over all other atoms.
>
> Is there any way to tabulate the energy functional of such local 
> electron density?

Since it depends only on inter-atomic coordinates, it should be 
possible. Before that, get some experience with normal GROMACS simulations.

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110628/674b17b6/attachment.html>