[gmx-users] functional form of PRODRG dihedrals

Jennifer Williams Jennifer.Williams at ed.ac.uk
Tue Dec 8 14:28:55 CET 2009


I have a general question re the PRODRG server used to create  
topologies for gromacs.

Using PRODRG for a simple alkane I get:

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
    4   3   2   1   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAG  CAE  CAC

The dihedrals created are given the function fu = 1 so I assume that  
they are not Ryckaert-Bellemans functions (where fu=3).

What is the functional form of the dihedral given by PRODRG? Does it  
correspond to equation 4.6.1 on page 62 of the gromacs manual (v. 4.0)?

If so which numbers in the above dihedral correspond to the symbols in  
equation 4.6.1?



Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
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