<div style="font-family: 'Times New Roman'; font-size: 16px;"><br /><br /><span>On 01/22/10, <b class="name">Gianfranco Bocchinfuso </b> <gianfranco.bocchinfuso@uniroma2.it> wrote:</span><blockquote cite="mid:001501ca9ac3$51f2d750$f5d885f0$%bocchinfuso@uniroma2.it" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word"><p>
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<p class="MsoNormal"><span lang="EN-US">Hi,<o:p _moz-userdefined=""></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p _moz-userdefined=""> </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 _moz-userdefined=""></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 _moz-userdefined=""></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 _moz-userdefined=""></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">What could be the origin of this
difference? </span></p></div></td></tr></tbody></table></p></span></div></blockquote>Your description does not sound self-consistent. Why do you have two topologies with indole atoms with zero charges, when your introduction described one with zero charges and one with normal charges?<br _moz_dirty="" /><br _moz_dirty="" />Note that energy group exclusions exclude non-bonded interactions, not merely electrostatic ones.<br _moz_dirty="" /><br _moz_dirty="" />A correct procedure for finding the electrostatic part of force components is to do a fully normal mdrun -rerun, and one with zeroed charges for the indole group, and subtract the force components so produced. Use gmxdump to compare your two .tpr files for what the actual differences are. Alternatively, alter a topology to have no bonded interactions, and make a version of the ffxxxnb.itp file with zero VDW parameters, grompp that, and do one mdrun -rerun with suitable energygroup-exclusions to make it run fast and correctly.<br _moz_dirty="" /><br _moz_dirty="" />Whether that means anything in the context of an MM forcefield that wasn't parametrized to reproduce such components is unknown.<br _moz_dirty="" /><br _moz_dirty="" />Mark</div>