Hi,
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 Gianfranco
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