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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Dec 7 22:23:15 CET 2006

> I am puzzled about this. In your opinion, when I  use  genpairs=no, fudgeLJ=
> 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful?
> On the other hand, when using genpairs=yes, how to set the scaling factor of
> fudgeLJ and fudgeQQ?$

fudgeQQ is always used no matter what the value of genparis is.

(exerpt from  
Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these
apply to the information outlined above. For example, gen-pairs does NOT mean
"generate a [ pairs ] section for the molecule." Instead, it means "If LJ-14
epsilon and sigma are not present in a [ pairs ] section entry, and  
that type of
interaction is not explicitly formulated in [ pairtypes ], then it is
permissible to use the regular non-bonded parameters, and in that case scale
them by FudgeLJ."

Therefore your settings indicate that coulombic 1-4 interactions will  
be scaled by 0.8333 and the pairs must be taken directly from the [  
pairs ] or [ pairtypes ] section (and they will NOT be scaled by  
fudgeLJ). In your case fudgeLJ does not matter (you could change the  
value and it would not affect your simulation). However, I have always  
hoped that it is set to 0.5 to indicate that this is what the  
forcefield developers have done for you and included it in [ pairtypes  
] so that it's kind of a reference value for your piece of mind.

I was assuming that the previous messages were from an Amber  
forcefield. Since Amber uses (to my knowledge) [ pairtypes ] instead  
of genpairs=yes, I was confused by the combination of genpairs=yes and  

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