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From: David A Case via AMBER <amber.ambermd.org>

Date: Thu, 29 Sep 2022 13:13:26 -0400

On Thu, Sep 29, 2022, Rosellen, Martin via AMBER wrote:

*>
*

*>I want to investigate the dynamics of monomers in a hexamer. Therefore,
*

*>I would like to define a plane (or two vectors) for each monomer and
*

*>calculate the angles of neighbouring monomer planes. I had a look at the
*

*>‘vector’ function where I can define a vector from centres of mass atom
*

*>mask1 to atom mask2, which is not optimal in my case.
*

*>
*

*>‘vector corrplane’ seems to be related since its description goes like
*

*>this: “corrplane: This defines a vector perpendicular to the (least-squares
*

*>best) plane through the atoms in <mask1>.”
*

*>
*

*>What I actually want from this is the "(least-squares best) plane through
*

*>the atoms in <mask1>”. In theory, I could rotate that vector back to be
*

*>parallel with the plane again and define second vector by rotating this
*

*>vector 90 degrees in the plane. I hope there is an easier solution.
*

I think what is already there is what you really want. The way to

define a plane is the specify a vector that is perpendicular to it;

(there are an infinite number of vectors parallel to the plane.) Then, the

angle between two planes *is* the angle between the vectors perpendicular to

the two planes.

...hope this helps....dac

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Received on Thu Sep 29 2022 - 10:30:03 PDT

Date: Thu, 29 Sep 2022 13:13:26 -0400

On Thu, Sep 29, 2022, Rosellen, Martin via AMBER wrote:

I think what is already there is what you really want. The way to

define a plane is the specify a vector that is perpendicular to it;

(there are an infinite number of vectors parallel to the plane.) Then, the

angle between two planes *is* the angle between the vectors perpendicular to

the two planes.

...hope this helps....dac

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Received on Thu Sep 29 2022 - 10:30:03 PDT

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