[gmx-users] .itp file for an electrode

Kukol, Andreas a.kukol at herts.ac.uk
Wed Jun 3 10:36:04 CEST 2009

It is not very difficult to construct a topology (itp-file) for one atom. You may look at the definitions of sodium or chloride in the .rtp file for the force field you want to use and adapt them to your needs.

Then you need the atom coordinates of the two parallel lattices, which you can make with genconf starting from a one atom coordinate file.



From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Negar Ashari Astani
Sent: 03 June 2009 09:22
To: gmx-users at gromacs.org
Subject: [gmx-users] .itp file for an electrode

Hello everbody

I'm trying to repeat a simulation which is reported in a paper. I'm going to model an electrode according to this exact method reported in this paper "the electrodes were modeled as two parallel XY square lattices made of charged Lennard-Jones spheres with radii 0.11 nm. Surface charge densities on the electrodes  were varied  by the partial  charge of the lattice spheres."
I'm looking for the .itp file for a metalic electrode.
Does anyone by any chance have such a file?

Thank you all so much

Negar Ashari Astani

More information about the gromacs.org_gmx-users mailing list