[gmx-users] How to include bonded parameters in ffgmxbon.itp?
lindahl at stanford.edu
Tue Sep 24 00:25:42 CEST 2002
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
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
When it comes to the dihedrals, it's important that you choose a
potential that is consistent with your treatment of 1,4 interactions, so
if you use Gromos96 nonbonded parameters I would recommend the Gromos96
dihedrals too (instead of e.g. OPLS).
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