Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - n*phi_o)]
^ this whole equation is Dreiding ^this whole equation is
Dreiding converted to the form in Gromacs
This would mean that:
0.5k in Dreiding = k in Gromacs
n in Dreiding = n in Gromacs
n*phi_o +180 in Dreiding (original form) is phi_s in the Gromacs notation
from the original post
I hope this makes sense!
Laura
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: 15 November 2012 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Dihedral form
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
er...@xray.bmc.uu.se
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