Thank you as well Jason.
On Sat, Feb 20, 2016 at 8:27 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sat, Feb 20, 2016 at 7:29 PM, Joel Lapin <jlapin.ncsu.edu> wrote:
>
> > Thanks a lot Daniel. My only issue is that each coordinate in the
> original
> > matrix corresponded to an x, y or z component of a specific atom, so
> > wouldn't that mean that each eigenvector corresponds to an x, y or z
> > component of a specific atom?
>
>
> No. The standard coordinate space for molecules is x1, y1, z1, x2, y2,
> z2, ..., xN, yN, zN (a 3-N dimensional space). The diagonalized covariance
> matrix defines a basis set of motions that is some sort of linear
> combinations of the original basis set (i.e., the cartesian coordinates for
> each atom individually). The eigenvectors are basically the projection of
> each original basis vector along the *new* basis vectors (each of the
> eigenvectors).
>
> It's a change in coordinate system from the arbitrary (but easy to
> conceptualize) cartesian space of each atom to a coordinate system that
> more fully describes your system.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 20 2016 - 18:00:03 PST
