[gmx-users] [Fwd: question about the torsional potential]

David van der Spoel spoel at xray.bmc.uu.se
Sat Dec 20 21:23:35 CET 2008

David van der Spoel wrote:
> I'm very new in the world of gromacs, but I have experience in
> simulation (Molecular Dynamics, Monte Carlo, Langevin Dynamics, etc)
> always using my own programs. Now I am starting a research in
> polyaniline (PANI) using GROMACS with a model potential that has been
> deduced from fisrt principles by my colleagues. This potential has
> stretching, bending, non bonded interaccions, etc. In principle I do
> not have problems to modify the ffG53a6bon.itp file introducing our
> new parameters, but I have a conceptual doubt when I would modify the
> angle of the dihedral potential. The problem is only conceptual
> because I do not
> know how this potential has been introduced in the code (fortran or c)
> of the program. I mean that I do not know if in the code has been used:
> 1) the formula 4.60 (page 54 of  version 3.3 of the gromacs manual)
> V(fi) = k*(1+cos(n*fi-fi0))
> where K is the force constant, fi0 is the reference angle that
> normally is 0 or 180 and n the multiplicity. In my case I use n = 2
> (two minima)
> 2) or the formula (13) that appears in the Journal of Computional
> Chemistry volume 25, page 1659 (2004)
> V(fi) = k(1+cos(delta)*cos(n*fi))
> where delta is 180 or 0
> Then if the dihedral potential has been introduced using the first
> possibility I can change easily the file ffG53a6.itp changing the
> angle fi0 (180 or 0) by the angles that suggest my colleagues.
> However if the potential has introduced using the second option then I
> suppose things could be more complicated and I supose that I should
> introduce dihedral restraints or something like that. Then the problem
> is that I do not know what kdihr constant I should use. Thank you very
> much for your attention, yours sincerely
> Manel Canales
You may be better off using the OPLS rtp as a template and using 
Ryckaert-Bellemans (cosine series) dihedrals.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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