[gmx-users] electrostatic forces

Berk Hess gmx3 at hotmail.com
Fri Jan 22 09:11:17 CET 2010


I guess this is caused by the 1-4 interactions.
These also contain electrostatic interactions, which are turned off when
you turn off the charges, but not by the energygrp_excl option.


From: gianfranco.bocchinfuso at uniroma2.it
To: gmx-users at gromacs.org
Date: Thu, 21 Jan 2010 18:58:14 +0100
Subject: [gmx-users] electrostatic forces



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



Thank you 



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