[gmx-users] Dihedral form

[Erik Marklund]

You could shift the reference angle by pi, which changes the sign of the cosine.

Best,

Erik

15 nov 2012 kl. 14.25 skrev Laura Leay:

> All,
> 
> I would like to parameterise the Dreiding force field for use with Gromacs. One thing I am not sure about is how to parameterise the dihedrals
> 
> The Dreiding paper has the form;
> 
> E= 0.5k { 1 - cos[ n( phi - phi_o)]}
> 
> However I cannot find this form in the Gromacs manual. The closest I can find in the Gromacs manual is:
> 
> E = k [ 1 + cos(n*phi - phi_s) ]
> 
> 
> Does anyone know of a way to use the Dreiding form in Gromacs, or to convert to a form that is more suitable for use with Gromacs?
> 
> Many thanks,
> Laura
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html