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On 4/05/2011 8:08 AM, Sikandar Mashayak wrote:
<blockquote
cite="mid:BANLkTikxD7Qoevd5d0kYfe3BXJMYwAuQZQ@mail.gmail.com"
type="cite">yeah, it says PME cant be excluded using energy
exclusion, so I am wondering about any other way to exclude it?<br>
</blockquote>
<br>
There is none.<br>
<br>
One option is to run the simulation with PME for the improved
sampling accuracy, and then to use mdrun -rerun with some other
electrostatics method if you really think these forcefields'
non-bonded interactions can be decompose groupwise and end up
meaning something.<br>
<br>
There was an approach posted in the last month or two that does
multiple reruns with PME to achieve the same effect.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikxD7Qoevd5d0kYfe3BXJMYwAuQZQ@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Tue, May 3, 2011 at 5:01 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5"><br>
<br>
Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi<br>
<br>
I want to compute only the non-bonded ( LJ + EL)
interactions between Protein and Solvent and exclude
non-bonded interactions between Protein Protein &
SOL SOL. <br>
But energy exclusion group does not necessarily exclude
the non-bonded electrostatic interactions while using
PME option for coulombtype. <br>
So I am just wondering if I were to compute
electrostatic interactions between just Protein SOL with
PME, how can I do that?<br>
<br>
</blockquote>
<br>
</div>
</div>
Hasn't this already been answered?<br>
<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
thanks<br>
sikandar<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080"
target="_blank">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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