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

David van der Spoel spoel at xray.bmc.uu.se
Sat Dec 20 21:20:38 CET 2008

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

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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