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<p class=MsoNormal><span lang=EN-US>Hi,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>I would like to calculate the electrostatic
forces on the atoms of an Indole group (in a TRP residue). <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>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). <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>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.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>What could be the origin of this
difference? <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thank you <o:p></o:p></p>
<p class=MsoNormal><span lang=EN-US>Gianfranco<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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