This must be specific to charmm's implementation in gromacs? Out of curiosity, why can one not use charge groups ?<div><br><div class="gmail_quote">On Tue, Mar 22, 2011 at 2:45 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>
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maria goranovic wrote:<br>
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Dear List<br>
<br>
I was looking at the charged groups in a charmm nucleotide, and could see several groups containing 4 to 14 atoms with integer charges. However, the default topology does not have these charged groups. each atom is given a charged group in the default topology. Can we foresee any problems in replacing the default charged groups generated by pdb2gmx by custom-made charged groups of integer values ? Along the same lines, will this lead to a significant increase in performance, besides the advantage of transferability ? <br>
</blockquote>
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With the CHARMM force field, you should not use charge groups. Each atom should be its own "group."<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanking you in advance<br>
<br>
Maria<br>
<br>
<br>
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-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
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</blockquote>
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-- <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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</font></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
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