<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Thank you Justin for your response<br></blockquote><div><br>I have tried
g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command<br>
<br>g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output <br><br>c6 = 4.66239e-03, c12 = 4.44320e-06<br>sigma = 0.31370, epsilon = 1.22310<br>Van der Waals minimum at 0.352116, V = -1.2231<br><br>
Fit of Lennard Jones (12-6) to Buckingham:<br>A = 199065, B = 34.0796, C = 0.00466239<br><br>Back Off! I just backed up potje.xvg to ./#potje.xvg.8#<br><br>gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)<br>
<br><br>Did I miss something ? <br><br>Thank you again for your help<br><br>SA<br><br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
sa wrote:<br>
> Dear All,<br>
><br>
> I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff<br>
> for a new atom type and incorporate them in my ffnonbonded.itp. Does<br>
> anybody know the mathematical expressions used to obtain these terms<br>
> from a sigma (nm) and an epsilon (kj/mol) values manually.<br>
><br>
<br>
g_sigeps can do this for you. Otherwise, you can convert between the two common<br>
forms of the Lennard-Jones equation.<br>
<br>
-Justin<br>
<br>
> Thank you for your help.<br>
><br>
> SA<br>
><br>
<br>
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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> | (540) 231-9080<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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