Thanks a lot Daniel. My only issue is that each coordinate in the original
matrix corresponded to an x, y or z component of a specific atom, so
wouldn't that mean that each eigenvector corresponds to an x, y or z
component of a specific atom? Its eigenvector is its covariances with all
other atom coordinate variances and its eigenvalue is its projection along
that eigenvector? So I am still trying to understand the physical
interpretation of every eigenvector.
On Sat, Feb 20, 2016 at 6:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sat, Feb 20, 2016 at 4:10 PM, Joel Lapin <jlapin.ncsu.edu> wrote:
> > matrix. My understanding of analyzing this matrix is that the largest
> > eigenvalues are your most significant degrees of freedom, which is simple
> > enough. The only issue is that the eigenvalues are perfectly sorted,
> which
> > doesn't make much sense to me. This would imply that the majority of
> > fluctuation in my protein happens at one end, while little to no
> > fluctuation happens in the rest of the protein.
>
> That's not really how you should interpret your eigenvectors. The
> eigenvectors when calculated from a coordinate covariance matrix
> describe *collective motions* in your system; the eigenvector
> associated with the largest eigenvalue is the motion with the biggest
> variance, the second largest eigenvalue the motion with the
> second-largest variance, and so on. It's not necessarily localized to
> a certain part of your system, although it could be. To know for
> certain you can either visualize a particular eigenvector (aka
> principal component in this case) with 'modes trajout', look at a
> "porcupine" visualization via the NMwiz plugin for VMD with
> 'diagmatrix nmwiz' output, or look at where fluctuations are occurring
> with output from 'modes fluct' etc.
>
> Hope this helps,
>
> -Dan
>
> >
> > Can someone please help me physically interpret this covariance matrix in
> > terms of which degrees of freedom are most significant in my protein?
> >
> > Thank you
> > Joel
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Sat Feb 20 2016 - 17:00:04 PST
