Hi, I am doing simulation of 864 D2O molecules using gromacs-4.5.5 version. I need to calculate the average electrostatic field on the deuterium atom in each time step.
I have used spce model of water and treat them as rigid by commenting out the -DFLEXIBLE statement in the mdp file. Further the force field I am using is OPLSAA and the non-bonded parameters for hydrogen are zero in this force field. So, the only force that hydrogen atoms should feel is electrostatic. Am I right? Then I converted the .gro file generated for water to deuterium using -deuterate utility and run the simulation. The forces on each deuterium is calculated by indexing the deuterium and using g_traj utility. Now if I am right above, then this force should be purely electrostatic. I calculated the magnitude of force on each deuterium atom and averaged it over the number of atoms in each time step. In order to calculate the electrostatic field I divided this force by the charge of hydrogen in the spce model. Is this the correct way to calculate electrostatic field on deuterium atom of rigid D2O. If I am going wrong anyway, then suggestions for calculating the same in gromacs. Regards, Biki -- View this message in context: http://gromacs.5086.n6.nabble.com/average-electric-field-on-hydrogen-deuterium-as-a-function-of-time-from-MD-of-water-D2O-tp5005100.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list 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! * 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/Support/Mailing_Lists