[gmx-users] questions related to genpairs=no

Wusheng Zhu zhuwu at bc.edu
Mon Feb 13 22:25:27 CET 2006

Dear All,
I am trying to set combination rule =3 and genpairs=no in the [default] 
part. I have two questions:
(1) when I listed explicit [pairtypes] or [pairs], what parameters 
should follow each pairs atomA-atomB ? Are they simply epsilon_AB and 
sigma_AB  calculated by combination rule, or should one of they be 
scaled multiplying with Fudge factors such as epsilon_AB*FudgeLJ and the 
other one simply be sigma_AB?
(2) Where to define FudgeQQ for 1-4 pairs Coulomb interaction as there 
are only two LJ parameters V,W (epsilon, sigma) following the pairs list 
based on the manual? So basically, how to put FugeLJ and FugeQQ into the 
topology file when genpairs=no?
Thank you in advance for any advice.

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