Re: [gmx-users] Electric field, potential, dielectric constant
Hi, You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose. Ran Vladimir Lankevich wrote: Dear Gromacs Users, I have several questions about electrostatics in Gromacs. I am simulating two proteins in water, separated by certain distance, and was interested in their electrostatic interactions. I was wondering if Gromacs can calculate and show me values of electric field or electric potential at any point within the volume. If yes, how can this be done? I looked through the manual and did not find much. I tried using g_potential, but it only gives me ten values for electric field (if I use 10 slices, and particular direction). This confused me, because I thought that in the system each coordinate would have different electric field. How should I interpret the results of g_potential? Also, can I use Gromacs to compute dielectric constant of a particular region within the volume? How can I do that? Thank you very much!! Cheers, Vladimir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Electric field, potential, dielectric constant
Dear Gromacs Users, I have several questions about electrostatics in Gromacs. I am simulating two proteins in water, separated by certain distance, and was interested in their electrostatic interactions. I was wondering if Gromacs can calculate and show me values of electric field or electric potential at any point within the volume. If yes, how can this be done? I looked through the manual and did not find much. I tried using g_potential, but it only gives me ten values for electric field (if I use 10 slices, and particular direction). This confused me, because I thought that in the system each coordinate would have different electric field. How should I interpret the results of g_potential? Also, can I use Gromacs to compute dielectric constant of a particular region within the volume? How can I do that? Thank you very much!! Cheers, Vladimir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
