thank you for the reply. That settles that.<br><br><div class="gmail_quote">On Tue, Mar 22, 2011 at 2:56 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ?<br>
</blockquote>
<br>
</div><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
<br>
On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
maria goranovic wrote:<br>
<br>
Dear List<br>
<br>
I was looking at the charged groups in a charmm nucleotide, and<br>
could see several groups containing 4 to 14 atoms with integer<br>
charges. However, the default topology does not have these<br>
charged groups. each atom is given a charged group in the<br>
default topology. Can we foresee any problems in replacing the<br>
default charged groups generated by pdb2gmx by custom-made<br>
charged groups of integer values ? Along the same lines, will<br>
this lead to a significant increase in performance, besides the<br>
advantage of transferability ?<br>
<br>
<br>
With the CHARMM force field, you should not use charge groups. Each<br>
atom should be its own "group."<br>
<br>
-Justin<br>
<br>
<br>
Thanking you in advance<br>
<br>
Maria<br>
<br>
<br>
<br>
-- Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><br>
<tel:%28540%29%20231-9080><div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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Technical University of Denmark<br>
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</div></blockquote><div><div></div><div class="h5">
<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 href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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