[gmx-users] functional form of PRODRG dihedrals

[Justin A. Lemkul]

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

-- 
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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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