Jennifer Williams wrote:
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).
Correct, function type 1 is a periodic dihedral, per the normal requirements of
the GROMOS force fields, for which PRODRG is intended.
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)?
Yes.
If so which numbers in the above dihedral correspond to the symbols in
equation 4.6.1?
Please see Table 5.4 in the manual.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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