[gmx-users] Dihedral form

[Mark Abraham]

And get the use of radians right!

Mark
On Nov 15, 2012 4:01 PM, "Erik Marklund" <erikm at xray.bmc.uu.se> wrote:

> Hi,
>
> 15 nov 2012 kl. 15.41 skrev Laura Leay:
>
> > 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 think that's correct.
>
> >
> > I hope this makes sense!
> >
> > Laura
> >
> >
> > ________________________________________
> > From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Erik Marklund [erikm at 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
> > erikm at xray.bmc.uu.se
> > http://www2.icm.uu.se/molbio/elflab/index.html
> >
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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
>
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