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From: Arun Srikanth <askforarun.gmail.com>

Date: Mon, 20 Oct 2014 00:45:08 -0400

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
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Sun Oct 19 2014 - 22:00:02 PDT

Date: Mon, 20 Oct 2014 00:45:08 -0400

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:

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sun Oct 19 2014 - 22:00:02 PDT

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