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

[Alexandre Suman de Araujo]

But my problem is not the bond lenght, this value I have. But the problem is
the K parameter... where can I find or calculate it for each type of atom?!
Thank's!

[]'s
Alexandre Suman de Araujo
IFSC - USP - São Carlos
UIN: 6194055
----- Original Message -----
From: "K.A. Feenstra" <Feenstra at chem.vu.nl>
To: <gmx-users at gromacs.org>
Sent: Tuesday, September 24, 2002 12:51 PM
Subject: Re: [gmx-users] How to include bonded parameters in ffgmxbon.itp?


> 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 |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
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