On Tue, Feb 24, 2015, James Starlight wrote:
>
> I have a question regarding collective dynamics calculations using normal
> mode analysis and principal components analysis made in case when 1) NMA
> was performed just based on one reference structure and 2) PCA was
> performed for the md trajectory where each frame has been superimposed
> against that reference structure. Eventually I've found good correlations
> (which means that it has the same directions) in the lowest-frequency modes
> from 1) and first PCs made for 2) as was obtained by means of dot product
> of both eigenvectors sets. Could someone explain me briefly why such
> correlation is exist?
Both methods are finding directions of motion that have low energy penalties
for movement in that direction, so it is not surprising that the results will
be quite similar. To the extent that the potential energy surface is
harmonic, the two methods are equivalent.
...dac
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Received on Tue Feb 24 2015 - 15:00:04 PST
