[gmx-users] torsion potential with 7 parameters

[Xavier Periole]

Hi Angel,

> If the transformation can not be analytical, I could fit (numerically)
> the parameters of the Ryckaert-Belleman potential to the function that
> results from the original one... Although this is not probably the best
> way of using the force field as originally proposed, the difference
> should be negligible.

If the fit to a Ryckaert-Belleman potential does not satisfy you, the
tabulated potentials should work fine. I never used it but I believe
it is a good solution and straightforward to use.

> Another alternative is to edit the code to introduce the new function,
> but I guess this is not trivial, any tip on this?

This should be your last and desperate solution ... but is certainly
feasible.

Best
XAvier

> 
> Angel Pineiro.
> 
> 
> On Wed, 2008-01-30 at 22:26 +1100, Mark Abraham wrote:
>> > Ángel Piñeiro wrote:
>> >> Dear David
>> >> I have taken a look to the manual (version 3.3) and I haven't found
>> >> information about how to tabulate bonded potential functions (it seems
>> >> that Ran is right). On the other hand, what do you mean exactly with
>> >> adding two dihedrals?
>> > It could well be that you'll have to wait for 4.0 for the tabulated
>> > dihedrals.
>> >
>> > You can however specify two torsion potentials around the same bond.
>> > This is how it is done routinely in CHARMM, where there are even more
>> > than two for some torsions.
>> 
>> Yep, although with sufficiently cunning trigonometry, you can reduce any
>> combination of those to one Ryckaert-Belleman dihedral. This doesn't help
>> for n >= 6, however.
>> 
>> Mark
>> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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