[gmx-users] dihedral potential
manel.canales at upc.edu
manel.canales at upc.edu
Sat Dec 20 18:01:17 CET 2008
Dear friends and Mark
Thank you very much for your answer. I mean polyaniline (PANI).
Obviously I have not mentioned the other parameters of the potential
(stretching, bending, non bonded interaccions, etc), because I know
how to modify the itp files in order to include the values of my
model. However I have problems to modify the
parameters 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.
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 *.itp. Thank you very much
for your attention
Manel Canales
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