[gmx-users] essential dynamics

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 17 10:34:58 CEST 2010

Hi Pawan,

This goes beyond a few lines of explanation. Move away from the tools
g_covar and g_anaeig slowly ;) and do some more background reading on
principal component analysis. I've tried to explain it in my tutorial
at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which
will probably answer your questions) and there are many documents on
the internet describing PCA as a statistical tool.



On Tue, Aug 17, 2010 at 9:56 AM, pawan raghav <pwnrghv at gmail.com> wrote:
> Hi all,
> I have a confusion regarding "Essential Dynamics". I have read so many
> papers regarding PCA and ED most of the papers among them explained
> eigenvectors and eigenvalues are as follows:
> if a protein has 207 C alpha residues then the total no of eigenvectors are
> 3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means
> that an eigenvector represents an C-alpha residue?
> But manual described that representations the direction of motions.
> But 3N X 3N is a covariance matrix that means this represents 621 X 621
> eigenvectors is it true?
> Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2,
> is it mean to plot a 2d graph between first two C-alpha atoms or first two
> structures?
> Please clearify me where I was wrong.
> The 2d graph shows oval and random large trajectory graph which represents
> the independent and dependent motion, may I know what does it mean?
> --
> Pawan
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands

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