FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
lindahl at cbr.su.se
Tue Feb 13 21:20:14 CET 2007
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).
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