[gmx-users] Making two defaults sections compatible

[David van der Spoel]

Steven Kirk wrote:
> Hello,
> 
> 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.
________________________________________________________________________
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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