Just one more question guys. Does the physical interpretation of any row or
column index still correspond to a specific atom coordinate, as it does in
the construction of the original covariance matrix?
On Sat, Feb 20, 2016 at 8:33 PM, Joel Lapin <jlapin.ncsu.edu> wrote:
> 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
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>
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Received on Sat Feb 20 2016 - 20:00:03 PST
