[gmx-users] average electrostatic field on deuterium atoms during simulation of D2O

biki bikramjit_101 at yahoo.com
Sat Feb 2 08:01:31 CET 2013

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 flexible by commenting out the -DFLEXIBLE statement in the mdp file. Further the force field I am using is OPLSAA and the LJ parameter 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 added all the three components 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.


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