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
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Edinburgh, EH9 3JL, United Kingdom
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