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@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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > 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@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
