Thanks! I will investigate about that
On Tue, Nov 22, 2016 at 12:26 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Nov 22, 2016 at 9:54 AM, The Cromicus Productions <
> thecromicusproductions.gmail.com> wrote:
>
> > Hi everyone!
> > I'm able to compute the principal components of a given trajectory using
> > PCAsuite.
> > http://mmb.pcb.ub.es/software/pcasuite/pcasuite.html
> > Then, I can convert them into pdb files and watch the motions.
> > PCAsuite also gives me the eigenvalues, so I know which are the most
> > important.
>
>
> > Now, if I understand correctly, the principal components are some
> "chosen"
> > normal modes which summarize the information of the trajectory, but how
> do
> > I know which normal mode is associated to each component I get? In
> > particular, I would like to know what is the associated vibration
> frequency
> > of each of the components.
> >
> ​​
> ​PCA and normal modes are very different. The "modes" in PCA are
> eigenvectors of the covariance matrix. The modes in NMA are eigenvectors
> of the Hessian matrix. They *can* contain similar information, but there
> is not a 1:1 correlation between PCA modes and normal modes.​ There are
> large operational differences, too -- for instance, PCA requires an
> ensemble of 'snapshots' (a rather *large* ensemble), whereas NMA requires a
> single *minimized* structure.
>
> Using PCA (more specifically using the mass-weighted covariance matrix
> rather than the standard covariance matrix) as approximations of
> vibrational modes is referred to as the "quasi-harmonic approximation". I
> would suggest starting there and scanning the literature.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Tue Nov 22 2016 - 11:00:03 PST
