Dear All, <br><br>Finally, I resolved my problem by contacting the author of the paper (thanks to D. Poger). They gave me the correct value for the epsilon and sigma (0.2137 nm instead of 0.3137 nm in the paper). <br><br>
SA<br><br><br><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;"><br>
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Message: 2<br>
Date: Tue, 29 Mar 2011 09:45:34 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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:4D910F8E.8050400@anu.edu.au">4D910F8E.8050400@anu.edu.au</a>><br>
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<br>
On 29/03/2011 12:17 AM, sa wrote:<br>
><br>
> OK, Pr van der Spoel,<br>
><br>
><br>
> So what is the correct way to obtain LJ C6 and C12 values given in the<br>
> [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp<br>
> if I have only the sigma and epsilon values.<br>
><br>
> If understand well [ atomtypes ] section give the comb-rules for the<br>
> atom with itself, correct ? And the nonbond_types section, the<br>
> comb-rules with the other atoms types.<br>
><br>
> So if I take into account only the OM atom, as an example, why I<br>
> obtained different values for C6 and C12 terms in the [ atomtypes ]<br>
> section.<br>
><br>
> Thank you again for your help.<br>
<br>
Section 5.3.3 of the manual goes through this.<br>
<br>
Mark<br>
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