[gmx-users] torsion potential with 7 parameters

[Xavier Periole]

On Fri, 01 Feb 2008 09:59:03 +0100
  Ángel Piñeiro <fangel at usc.es> wrote:
> Hi Xavier,
> I made the fit but to reproduce well the original function I needed a
> combination of two periodic functions with multiplicities non integer
> plus one Ryckaert-Belleman potential (12 parameters in total!). So I
> should put three contributions to each of these dihedrals in the
> itp's... I found this solution a bit forced although I guess it should
> work. However I have another problem: I need the itp to combine
> perfluoroalkanes (PFA's) with lipids, for which I have topologies in the
> gromos force field. Thus I decided to build a topology for the PFA's
> based on the gromos force field but taking some parameters (angles and
>FCCF dihedrals) from the Borodin (JPCB (106) 2002) Force Field. I have
> some experimental properties (estructural and thermodynamic) available
> for several PFA's that I can try to reproduce in order to check the new
> topologies. I hope this works!

Sounds good.

> Regarding the tabulated potentials, as far as I understood they are not
> implemented yet for bonded interactions, isn't it?

Indeed sorry!

> 
> Best regards,
> 
> Angel.
> 
> 
> On Fri, 2008-02-01 at 08:39 +0100, Xavier Periole wrote:
>> 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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> 
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-----------------------------------------------------
XAvier Periole - PhD

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