[gmx-users] electrostatic forces

Gianfranco Bocchinfuso gianfranco.bocchinfuso at uniroma2.it
Thu Jan 21 18:58:14 CET 2010



I would like to calculate the electrostatic forces on the atoms of an Indole
group (in a TRP residue). 

I have performed two reruns of my simulation with two different topologies :
a normal topology and a topology with all the Indole charges set equal to 0.
I have also added energygrp_excl = Indole Indole (to delete electrostatic
force inside the Indole) and also I have deleted in both topologies all the
pairs between atoms belonging to the Indole group (to delete the
electrostatic contribution coming from 1-4 interactions inside the Indole
group). Furthermore I have used a very simple mdp file (with cut-off,
without DispCorr etc.) to avoid contribution coming, for example, from ewald
summation. In these conditions I expected that the differences between the
forces computed in the two simulations were due only to the electrostatic
interactions with the other atoms of protein and with solvent (SPC). 

Checking the obtained forces I see that atoms of the Indole (i.e. the CD2
and CE2), with charges equal to 0 in both topologies, show different forces
in the two simulations.

What could be the origin of this difference?  



Thank you 



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