the phase shift and periodicity describe the shape of the curve that is
used for the dihedral correction. It does not necessarily have to be
related to anything about the measurement of the dihedral. Usually these
are used as free parameters (along with the amplitude) in fitting the
dihedral parameters. Since this cosine curve is not the actual energy
profile for rotation, but instead is the *difference* between the actual
energy and the energy described by all of the other force field terms, it
can be quite non-intuitive to just pick values.
On Tue, Jan 8, 2013 at 7:28 AM, <osalo.abo.fi> wrote:
> Dear Colleagues,
>
> In the frcmod file, is the phase shift always either 0 or +180?
> How do I know which one it should be for a particular dihedral that is
> for example -140 degrees when measured.
>
> In addition, I do not understand clearly the periodicity value...can
> it be for example 3.000 for all new dihedrals I define? (the system is
> quite rigid and there should not be full rotation around bonds in
> those dihedrals.
>
> Thank you very much for your help.
>
> Kind regards, Outi Salo-Ahen
>
> --
> Dr. Outi Salo-Ahen
> Åbo Akademi University
> Department of Biosciences, Biochemistry
> Tykistökatu 6 A
> FIN-20520 Turku
> E-mail: outi.salo-ahen.abo.fi
> Tel: +358-2-215 4009
> Fax: +358-2-230 5018
>
>
>
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Received on Tue Jan 08 2013 - 05:00:04 PST
