On Fri, 01 Feb 2008 09:59:03 +0100
Ángel Piñeiro <[EMAIL PROTECTED]> 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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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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