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<div>Sorry to but in on the conversation. Im between computers so cant track it down easy, (on my hard drive) but I did find one older publication comparing gromacs solvent (ion/buffers) effects with plasmon resonance calculated affinities, the results of that single paper showed the closer the solvent ion, etc...to the ones used in the wet experiments, the better the fit between affinity curves (protein-protein). Thus even the older software seemed to represent reality in some ways well...but I never ran across something that broke these down into energy components...thus would like to see the graphs out of curiosity...just a lit search for something I know exists...</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Samstag, 30. November 2013 um 18:01 Uhr<br/>
<b>Von:</b> "Mark Abraham" <mark.j.abraham@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org>, "Vitaly Chaban" <vvchaban@gmail.com><br/>
<b>Betreff:</b> Re: [gmx-users] Charge correction PME</div>
<div name="quoted-content">... but not necessarily any good! See<br/>
<a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html" target="_blank">https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html</a>.<br/>
I have seen Gerrit present some convincing results since then, but they do<br/>
not seem to be in press, yet.<br/>
<br/>
Neutralizing explicitly seems like the right course just about always!<br/>
<br/>
I'm never sure why people think extracting an energy component means<br/>
anything; extracting part of an intrinsically global one seems even less<br/>
likely to mean anything... Do enlighten me! :-)<br/>
<br/>
Mark<br/>
<br/>
<br/>
On Sat, Nov 30, 2013 at 5:29 PM, Dr. Vitaly Chaban <vvchaban@gmail.com>wrote:<br/>
<br/>
> I might be wrong here, but my expectation is that nowadays you should<br/>
> not do anything explicitly in this regard. The compensating charge is<br/>
> automatically applied.<br/>
><br/>
><br/>
> Dr. Vitaly V. Chaban<br/>
><br/>
><br/>
> On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila<br/>
> <benrezkallah@gmail.com> wrote:<br/>
> > Dear gmx_users,<br/>
> > My question is about the coulomb LR contribution with PME, I can't<br/>
> access<br/>
> > to david's original post treating this subject in the mailing list (<br/>
> > <a href="http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html</a>) if it<br/>
> > exists, because some links are disabled.If any one can send me the page?<br/>
> > I'm working on a protein in explicit solvent (water) at different<br/>
> > concentration of salt (NaCl).I need to calculate coulomb LR energy<br/>
> > interaction between some residues and Cl-/Na+.<br/>
> > My question is :should I turn off the charge correction ( when<br/>
> calculating<br/>
> > electrostatics for no neutral system),and how to do it? or it has a small<br/>
> > contribution to the energy, and I have no worry about it.<br/>
> ><br/>
> > I hope find answers in your replies.<br/>
> ><br/>
> > respectively,<br/>
> > Djamila Benrezkallah<br/>
> > University of Oran<br/>
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