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
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