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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110628/674b17b6/attachment.html ------------------------------ -- gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 86, Issue 188 ****************************************** -- 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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