On Sat, Feb 16, 2013, kurisaki wrote:
>
> In the contrast, can we consider the eigen vector with smaller eigen value
> represent fast mode, such like bond stretching between atoms?
> They could be ignored if we focus on global dynamics of protein.
> If so, it is clear that I should ignore such a fast mode.
PCA is independent of time, so it no notion of "fast" and "slow". It the
eigenvalue of the 306th vector isolated from other eigenvectors? If you
really want to investigate this, you should look at the character of this
eigenvector, and see if you learn anything from what atoms are moving.
It would also be of use to know how many atoms (or Ca atoms) are in your
system.
....dac
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Received on Sat Feb 16 2013 - 07:30:03 PST
