[gmx-users] Dihedral angles

David Cerutti dcerutti at mccammon.ucsd.edu
Tue Jun 1 10:11:37 CEST 2004


   I'm trying to reverse-engineer some of the GROMACS software to use its
potentials in some of my own calculations.  I'm particularly interested in
the dihedral angle potential parameters, and the "special" 1-4 LJ
parameters.  Does anyone know where to find these in the gromacs topology

* I'm reading ffgmxbon.itp, and I see [dihedral types].  Is q0 the phase
angle and cq the amplitude?  Does q correspond to phi and cq to kq in
equation 4.52 in the manual?

* When I look for the special 1-4 interactions, I find that there are
"c6/c12" and "cs6/cs12" parameters in ffgmxnb.itp.  Could I be so lucky as
to simply have to provide the cs6/12 parameters for the "special" LJ
parameters when considering proper dihedral LJ interactions?  Or is it
(gulp) more complicated? 

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