Hi all!
I've just copied my bellow post from another md mail-list where I've
started the same discussion:
here I've rose question regarding sensitivity of both methods in different
tasks. In case of NMA it should be based on the knowing that initial
structure is lied within the deepest minima along all its possible states
from the energy landscape => it means that we start to looking on the
softest transition pathways exactly from this point. On other hand in case
of PCA the results should be depends on full coverage of the analyzed
trajectory trajectory. So my question: It's not quite understand for me
why the directions of the first PCs (most collective modes calculated using
PCA from the covariance matrix) should be at the same time more softest
(less-energy consuming pathways) as in case of the NMA (where it's direct
consequence of the diagonalisation of the Hessian)?
Thanks for suggestions again!
James
2015-02-25 3:02 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
> 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 Thu Feb 26 2015 - 03:30:03 PST
