[gmx-users] How to include bonded parameters in ffgmxbon.itp?

[K.A. Feenstra]

Erik Lindahl wrote:
> 
> Alexandre Suman de Araujo wrote:
> > Hi GMXer
> >
> > I'm trying to include parameters to acetonitrile in ffgmxnb.itp and
> > ffgmxbon.itp. The Non-bonded parameters I can include using LJ parameters
> > and charges found in some papers. My doubt is how to find(or calculate)
> > bonded parameters to include in ffgmxbon.itp?
> >
> > Thank's and waiting answers
> >
> 
> Hi Alexandre,
> 
> First - bonded parameters in most forcefields are not that well
> determined; a lot of the are actually more or less intelligent guesses.
> 
> If you constrain the bonds, the actual force constant won't matter, only
>   the bondlength, so that removes one parameter. The bond distance between
> two atom types probably don't differ that much between force fields; the
> important thing is to browse the force fields and find atoms with
> similar environments.

Better if you can compare with crystal structure(s) of the molecule.
For many small molecules, there are quite accurate structures, and I
am sure acetonytrile will ba among those. Although, ofcourse, the 
values might not be optimal for liquids...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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