[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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