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
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Received on Sat Feb 20 2016 - 17:30:02 PST
