[gmx-users] GROMOS-96 proper dihedrals

[Dallas Warren]

Thanks for your earlier answer Eric :-)

Another question about the force fields .....

 From Scott et al. (1999), equation 52 is for dihedrals in the GROMOS 
format.  As constants it has the force constant, phase shift and 
multiplicity, with the variable being the dihedral angle.

In the dihedrals defined within ffG43a2xbon.itp for the GROMOS-96 force 
fields the dihedrals types are defined something like this:
         # first gd_number to define the G96 proper dihedral type
         # an angle in degrees, which I assume is theta max
         # some value, which I suspect is the force constant
         # and the multiplicity all on the same line
         # next line is a comment on which dihedrals it is appropriate for
         # then another number, this I suspect is the phase shift.

Am I correct in my interpretation of the lay out of the ffG43a2xbon.itp?

It doesn't make a lot of sense though (well the first three values do ;-) 
), since from table 5.3 and 5.4 in the GROMACS 3.1.1 manual, proper 
dihedrals are define in terms of theta max, force constant and multiplicity 
(also shown by equation 4.52).  There is no place for the phase 
shift?!?!  Isn't that implemented or used with GROMACS?

Another proper dihedral issue .... I get the feeling this has been brought 
up previously, but I can't happen to find it in the archives at the 
moment.  If you have more than one multiplicity and force constant for a 
proper dihedral, can you simply define two for the same proper dihedral? 
For example multiplicity of 1 and 2 with different force constants for each 
multiplicity.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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