[gmx-users] proper dihedral function!!! again!!!

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Apr 17 08:43:01 CEST 2003

>  And the function 4.52 is the most simplest function for dihedral 
> angles.I think it's not the Gromos 43a2's dihedral angles function,it's 
> Gromacs'. Now, I hope to know the difference of dihedral function between 
> Gromacs and Gromos.

 From what I can gather, there is no difference between the GROMACS and 
GROMOS dihedrals.  Both use an angle maximum, force constant and 
multiplicity to define the potential.  They also have a phase shift which 
you can implement in the equation, but no mention of this is made in the 
topology discussions or the manner in which you can use it if needed.

So if you use the GROMOS forcefields, then you define a dihedral 
type/number, something like gd_#.  If you look at table 5.3 the parameters 
that can be set for a proper dihedral is the angle maximum, force constant 
and then multiplicity.  Each gd_# has a defined angle maximum, force 
constant and multiplicity.

>   Second, if I want to use dihedral angle type 3,there are more than one 
> force constant in dihedral function.  In ffG43a2bond.itp, there is only 
> one force constant.Where can I put or find the other force constant?

By dihedral type 3, do you mean Ryckaert-Bellemans potentials?  If so, then 
there is only one that comes with the force fields, and this is for the 
CH2-CH2 dihedral optimised for alkanes.  The values for this is shown on 
page 89-90 of the manual.

If you want to use a R-B for other dihedrals, then you either have to 
generate them yourself, or I noticed that a couple of days ago someone 
mentioned that OPLS has more defined in it so you may be able to transfer 
some over from there.

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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