[gmx-users] torsion potential with 7 parameters

[Ángel Piñeiro]

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!

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

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
> >> 
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> -----------------------------------------------------
> XAvier Periole - PhD
> 
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php