[gmx-users] Making two defaults sections compatible
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 27 12:35:42 CEST 2006
Steven Kirk wrote:
> I'm using a macromolecule with the OPLS-AA force field, solvated with
> SSWM4-DP polarizable water (many thanks to DvS for this). The .itp file
> for the polarizable water has a [defaults] line that looks like:
> [ defaults ]
> LJ Geometric
> whereas when the OPLS-AA forcefield .itp files are read in, they contain
> a defaults section that looks like this:
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 yes 0.5 0.5
> and hence grompp complains about two [defaults] sections.
> I know comb-rule 3 means geometric averages of LJ parameters, but I'm
> wondering about the compatibility of the 'gen-pairs', 'fudgeLJ' and
> 'fudgeQQ' parameters.
> Can anyone suggest a single defaults line that would be compatible with
> both of these ? Could I safely use ONLY the OPLS-AA defaults line
> without breaking SSWM4-DP?
> Many thanks,
> Steve Kirk
Apart from just trying it, which I recommend you do, the SW models don't
have any 1-4 interactions so you are safe there. For more involved
molecules this may be a problem.
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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