AMBER Archive (2000)

Subject: Re: radius of gyration

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 11 2000 - 14:41:00 CDT

        We are trying to determine the rotation about a bond in the
        group R(R)N-O with respect to time. Carnal has a group
        operation called radius of gyration which seems like it should
        be useful for this purpose. But I'm not exactly sure what this
        command dumps ...

Look up the definition of radius of gyration - it has to
do with the compactness of the group, I believe.

        What are the units of this number, Angstroms,

Yes.

        and what is the reference point - is the center of mass used

Yes.

        Finally, is there a way to apply the radius of gyration to
        only the atoms of interest.

By defining a group containing those atoms. However, as I understand
the question, it would have no applicability to measuring rotation
around a bond; TORSION is what does this in carnal.

Bill Ross