<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;">OK, Pr van der Spoel, <br></blockquote><div><br>So what is the correct way to obtain LJ C6 and C12 values given in the
[ atomtypes ] and in
the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values. <br><br>If understand well
[ atomtypes ] section give the comb-rules for the atom with itself, correct ? And the nonbond_types section, the comb-rules with the other atoms types. <br><br>So if I take into account only the OM atom, as an example, why I obtained different values for C6 and C12 terms in the [ atomtypes ] section. <br>
<br>Thank you again for your help. <br><br>SA<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>
Message: 2<br>
Date: Mon, 28 Mar 2011 14:13:44 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] Re: mathematical expression to obtain the C6<br>
and C12 LJ terms for the GROMOSXX ff family<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4D907B78.20105@xray.bmc.uu.se">4D907B78.20105@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 2011-03-28 14.07, sa wrote:<br>
> Sorry I forget to say in my previous mail that the values obtained by<br>
> g_sigeps_mpi are not similar to the values given in<br>
> the GROMOS53A6 ffnonbonded.itp for the OM atom.<br>
><br>
> OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07<br>
Difficult to compare this way.<br>
note that gromos does not use simple combination rules.<br>
For OM there are different C12 (IIRC) depending on the interacting atom.<br>
You should look only at the<br>
[ nonbond_types]<br>
section<br>
><br>
> So your advices are welcome.<br>
><br>
> SA<br>
><br>
><br>
> 2011/3/28 sa <<a href="mailto:sagmx.mail@gmail.com">sagmx.mail@gmail.com</a> <mailto:<a href="mailto:sagmx.mail@gmail.com">sagmx.mail@gmail.com</a>>><br>
><br>
> Thank you Justin for your response<br>
><br>
><br>
> I have tried g_sigeps with the OM type LJ values (sigma (nm) =<br>
> 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper<br>
> (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't<br>
> retrieve the C6 and C12 values given for the same in the GROMOS53A6<br>
> 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>
> sa wrote:<br>
> > Dear All,<br>
> ><br>
> > I would like to compute the C6 and C12 LJ terms for the<br>
> GROMOS 53A6 ff<br>
> > for a new atom type and incorporate them in my<br>
> ffnonbonded.itp. Does<br>
> > anybody know the mathematical expressions used to obtain<br>
> 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<br>
> 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>
> --<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="http://vt.edu" target="_blank">http://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>
><br>
> ========================================<br>
><br>
><br>
><br>
><br>
</blockquote></div><br>