[gmx-users] Another dihedral angles question

David Cerutti dcerutti at mccammon.ucsd.edu
Sat Jun 19 03:45:51 CEST 2004

Boy, I must look like an idiot...

> I see dihedral angle potentials that need to be applied between O1 and the 
> CH3 united atom, N2 and the CH3 united atom, 01 and N, and N2 and N.  So,
> I'm going to compute the four dihedral angles I just described and plug
> them into (for the j,k atoms C and CA)
>    potential = kphi(C:CA)*cos(mult(C:CA)*angle-phi0(C:CA))
> and then I'll have to do something with the four pairs of i:l atoms, but
> I'm not sure how to use q0 and cq in that case even if parameters for
> these values are given for O1:CH3, N:N2, N2:CH3, and N:O1.

I mean 

     potential = cp(C:CA)*cos(1+mult(C:CA)*angle-phi0(C:CA))

but, I'm ready to be corrected on the multiplicity term, if that's not


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