[gmx-users] average electric field on hydrogen/deuterium as a function of time from MD of water/D2O
bikramjit_101 at yahoo.com
Sat Feb 2 13:19:00 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 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
If I am going wrong anyway, then suggestions for calculating the same in
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