Hello,
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?
Thanks
Jenny
Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861
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