[gmx-users] mixing rules for LJ parameters?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Dec 19 09:02:31 CET 2006
Nicolas Winter wrote:
> I'm trying to understand how the LJ parameters are determined in the
> Gromacs FF, namely the file ffgmxnb.itp. According to the mixing rules
> given on page 88 of the manual c6 and c12 for interactions between atoms
> should just be the square root of the product of the individual atom
> parameters. However when I tried to take the individual c6 and c12 for O
> and N for example, and mix them according to this rule I come up with
> the correct number for for the O - N c6 value, but /not /for c12. So I'm
> curious how the c12 is determined? Here are the numbers I'm working
> with, the individual atom parameters taken directly from the Gromacs FF,
> file ffgmxnb.tip. The O-N values are what I get from using the mixing
> rule combination 1 on p88.
Since this is a derivative of GROMOS87 mixing rules are not applied
systematically, that is, certain atom types have multiple (max 3) C12
depending on the interaction partner. You'll need access to GROMOS
documentation either 87 or 96 to get back to the original parameters.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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