[gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham)

[manana koberidze]

Thank you Mark, what puzzles me here is summation, if it was only one term
than it would be clear.

Generally, if there is no other way than changing the source code which
files must be modified?Is there any information about it anywhere? I found
just the list of files but for bonded interaction in the manual.

Thanks again


> 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
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-- 
Manana Koberidze

Graduate Student
Department of Applied Physics
Aalto University School of Science
P.O.Box 11100
FI-00076 AALTO
Finland
Tel: +358-9-470 23137
E-mail: manana.koberidze (at) aalto.fi
Office: Y229e main building (2nd floor)
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