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<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thank you for your reply,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Really, I don’t think that the difference come from the
1-4 interactions. <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I have excluded all the 1-4 interaction involving atoms in the
indole group (deleting them from the pairs list). Furthermore, I have added the
indole as an energygrps, and checking the 1-4 energy terms in this group, they
are correctly 0 both in the simulation with the charges and in the simulation
with charges=0<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Gianfranco<o:p></o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Segoe UI","sans-serif"'>Da:</span></b><span
style='font-size:10.0pt;font-family:"Segoe UI","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>Per
conto di </b>Berk Hess<br>
<b>Inviato:</b> venerd́ 22 gennaio 2010 9.11<br>
<b>A:</b> Discussion list for GROMACS users<br>
<b>Oggetto:</b> RE: [gmx-users] electrostatic forces<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>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<o:p></o:p></span></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>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<o:p></o:p></span></p>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Hi,</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> </span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>I
would like to calculate the electrostatic forces on the atoms of an Indole
group (in a TRP residue). </span><span style='font-size:10.0pt;font-family:
"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>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><span style='font-size:
10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>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><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>What
could be the origin of this difference? </span><span style='font-size:
10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> </span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Thank
you <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>Gianfranco</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> </span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p> </o:p></span></p>
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