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

[Mark Abraham]

On 29/06/2011 7:08 PM, manana koberidze wrote:
> Thank you Mark, what puzzles me here is summation, if it was only one 
> term than it would be clear.

But a normal Coulomb interaction has the form E_i = q_i * SUM{q_j / 
r_ij} summing over the other atoms j. If you can cast the electrostatic 
component of the energy into a form dependent only on the inter-atomic 
distance and atomic charge (as above) then using the tabulated 
non-bonded interactions already implemented in GROMACS is 
straightforward. See manual. If you need a different interaction for 
each pair of atom types, then that is doable, but you'll have to make a 
lot of energy groups and corresponding table files and accept 
not-very-good performance - but I don't think you need this.

Mark

> 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 <http://aalto.fi>
> Office: Y229e main building (2nd floor)
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