For Impropers I am not sure how amber defines the phi.
If I J L are on the same plane. It is the angle between I-J-L and I-K-J ?
In lammps it is clearly defined this way.
I,J,K,L - then the improper dihedral angle is between the plane of I,J,K
and the plane of J,K,L. Note that because this is effectively a dihedral
angle,
Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined
between the 4 atoms.
I have to equivalently convert to this form. This I can do but I need to
know how phi is defined for an improper in AMBER.
Arun
On Mon, Oct 20, 2014 at 12:27 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Oct 20, 2014, at 12:16 AM, Arun Srikanth <askforarun.gmail.com>
> wrote:
> >
> > Thanks i will keep point [1] in mind.
> >
> > Two questions
> >
> > In amber,
> >
> > 1. If I have a dihedral let's say I-J-K-L. How is phi calculated in the
> > dihedral potential expression. Is it the angle between the planes
> > containing
> > I-J-K and J-K-L
>
> Yes. More precisely, it is the angle between the normal vectors of those
> two planes (which is easy to compute via cross products of the two vectors).
>
> > 2. How is phi defined for an improper I-J-K-L with K as the central atom
>
> Same way.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Oct 19 2014 - 22:00:02 PDT
