On Tue, Feb 24, 2015 at 5:39 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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.
>
This is basically the relationship between the harmonic and quasi-harmonic
approximations to solute entropy commonly employed by MM/PBSA-type
analyses, if you are familiar with those.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 24 2015 - 18:30:02 PST
