[gmx-users] Re: fudgeQQ (again ...)

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Dec 7 21:11:29 CET 2006

> Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I
> added 1-4 pairs in [pairs] and then got the right values. I thought
> Gromacs would automatically find 1-4 pairs.

send the structure to pdb2gmx and the value of genpairs will be  
determined from your ffXXX.itp file. As far as I know, this is only in  
this way that the [pairs] section will be generated in the output.top  
file. If your system is not a protein, then you need to add the paris  
section (and in fact create the entire .top file) by hand.

By the way, why are you using the combination of genpairs=yes  
fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for  
any force field that comes in the standard gromacs distribution.

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