[gmx-users] Re: fudgeQQ (again ...)
lzheng at me.rochester.edu
Thu Dec 7 21:58:09 CET 2006
I'm using AMBER FF, so those are the scaling factors in this force
field. Actually I never used standard Gromacs/Gromos ff and always make my
own top file from scratch.
On Thu, 7 Dec 2006 chris.neale at utoronto.ca wrote:
>> 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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