[gmx-users] questions related to genpairs=no

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 14 08:54:36 CET 2006

Wusheng Zhu wrote:
> 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?

First of all you can check the result in the tpr file by using
gmxdump -s topol.tpr | less
and search for LJ14.

In the pairtypes or pairs section you probably can not give sigma and 
epsilon but have to compute the C6 and C12 directly. Please check using 
the above method.

You only need to specify pairtypes if they are different than what would 
be generated. FudgeLJ is *only* used with genpairs = no, otherwise you 
have full LJ interactions. FudgeLJ will modify the C12 and C6 params 
directly in the tpr file. FudgeQQ is used for 1-4 Coulomb interactions 
if you specify it in the topology. You will find the number back in the 
parameter section of the tpr file (and md.log file).

> Thank you in advance for any advice.
> Wusheng
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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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