FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)

[Erik Lindahl]

Hi,

On Feb 13, 2007, at 6:52 AM, Jones de Andrade wrote:

> Hi guys.
>
> Well, I'm not "exactly" trying t reopen an old discussion. I'm  
> trying to see a different aspect from it, as the subject indicates.
>
> Since the message reproduced below is the last of the "fudges"  
> questions, I'm worried about the fact of the fudgeLJ meaning  
> nothing for the simulation.
>
> First, is it true, and there is no way around to get a working  
> fudge LJ of 0.5 AND a fudgeQQ of 0.8333 in gromacs simulations?
>
No, you can certainly use fudge factors with Gromacs.

Essentially:

1. If you do not generate 1,4 ("pair") interactions they will be zero  
unless you specify them explicitly.
2. If you do generate them, standard combination rules of the force  
field will be applied, combined with the fudge factor.
3. If you generate pairs and still specify some interactions, those  
will override the generated values.

Cheers,

Erik