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

[Erik Lindahl]

Hi,

On Feb 13, 2007, at 8:31 PM, Jones de Andrade wrote:


>
> 1 - In a top file, have the lines like this:
> [ defaults ]
> ; nbfunc      com-rule    gen-pairs      fudgeLJ  fudgeQ
>    1            2          yes           0.5000  0.8333
> #include "ff_moleculeA.itp"
> #include "moleculeA.itp"
> [ system ]
> Pure A
> [ molecules ]
> ;molecule name   nr.
> moleculeA           256
>
> 2 - In the ff_moleculeA.itp file, it has the [atomtypes], [bondtypes],
> [angletypes] and [dihedraltypes] directives, in the standard way and
> with all potential parameters.
>
> 3 - In the moleculeA.itp file, I included:
> [ moleculetype ]
> ; Name                     nrexcl
> moleculeA                        3
> [atoms] directive, with atomic masses and charges included;
> [bonds], [angles] and [dihedrals] directives, *without* the potential
> parameters, just the atom indexes;
> And the [pairs] directive, with the "funct" included but *no* sigma or
> epsilon parameters. The following as an example:
> [ pairs ]
> ;  ai    al funct     sigma (nm)  epsilon (kJ/mol)
>    9     5     1
>   10     5     1
>   11     5     1
> ...
>
> Now, the question is: is it right, in a way that will use both the
> different valued fudgeLJ of 0.5, and the fudgeQQ of 0.8333 for 1-4
> interactions, or should I make any kind of correction still?
>
> Thanks a lot in advance for everything,


That should be fine, as long as your [pairtypes] section is empty  
(i.e., nothing that overrides your generated values).

Cheers,

Erik