Sorry for the confusion. Its clear now.
Thanks
Arun
On Mon, Oct 20, 2014 at 2:08 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, Oct 20, 2014 at 12:45 AM, Arun Srikanth <askforarun.gmail.com>
> wrote:
>
> > For Impropers I am not sure how amber defines the phi.
> >
>
> I answered that in my last email. It is defined exactly the same way as it
> is for proper torsions (in fact, they are done in the same subroutine).
>
> If I J L are on the same plane. It is the angle between I-J-L and I-K-J ?
> >
>
> No, like proper torsions, it is the angle between the planes defined by
> I-J-K and J-K-L.
>
> 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'm not sure what your point is here? Actually in Amber, the 3rd atom is
> the central atom (so the bonds I-K, J-K, and L-K exist).
>
> 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.
> >
>
> I'm confused. You say above that LAMMPS has some weird I-J-L, I-K-J
> definition for improper torsions, but then you say below that that the
> improper angle is defined between I-J-K and J-K-L, and that you have to
> convert to that latter definition.
>
> Since Amber uses the same functional form for improper torsions as it uses
> for proper torsions (unlike, for example, the CHARMM force field), the best
> approach IMO is to simply use the same subroutine for both kinds.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Oct 19 2014 - 23:30:03 PDT
