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Hi,<br><br>I guess this is caused by the 1-4 interactions.<br>These also contain electrostatic interactions, which are turned off when<br>you turn off the charges, but not by the energygrp_excl option.<br><br>Berk<br><br><hr id="stopSpelling">From: gianfranco.bocchinfuso@uniroma2.it<br>To: gmx-users@gromacs.org<br>Date: Thu, 21 Jan 2010 18:58:14 +0100<br>Subject: [gmx-users] electrostatic forces<br><br>
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<p class="ecxMsoNormal"><span lang="EN-US">Hi,</span></p>
<p class="ecxMsoNormal"><span lang="EN-US"> </span></p>
<p class="ecxMsoNormal"><span lang="EN-US">I would like to calculate the electrostatic
forces on the atoms of an Indole group (in a TRP residue). </span></p>
<p class="ecxMsoNormal"><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). </span></p>
<p class="ecxMsoNormal"><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.</span></p>
<p class="ecxMsoNormal"><span lang="EN-US">What could be the origin of this
difference? </span></p>
<p class="ecxMsoNormal"><span lang="EN-US"> </span></p>
<p class="ecxMsoNormal"> </p>
<p class="ecxMsoNormal">Thank you </p>
<p class="ecxMsoNormal"><span lang="EN-US">Gianfranco</span></p>
<p class="ecxMsoNormal"><span lang="EN-US"> </span></p>
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