The eigenvalues are printed in the output from the 'diagmatrix' (aka
'analyze matrix') command. The format of the 'eigenmodes' output is:
Eigenvector file: <type> nmodes <# of modes> width <data element width X>
<# avg coordinates> <vector size>
<Avg coordinates, 7FX.5 columns>
Then for each eigenmode/principal component:
****
<eigenmode number> <eigenvalue>
<eigenvector, 7FX.5 columns>
So in the line after each '****' the second column contains the
eigenvalue for the subsequent eigenvector. Note that if the matrix was
a mass-weighted covariance matrix the eigenvalue units are converted
from Ang^2*amu to cm^-1.
Hope this helps,
-Dan
On Mon, Sep 29, 2014 at 10:37 PM, Nicole Ippolito
<ippolito.nicole89.gmail.com> wrote:
> Hello Amber Community,
>
> I am calculating the percent common variance for PCA. I am wondering if
> there is a keyword in cpptraj to pull out the eigenvalues or if I need to
> do this manually.
>
> Thank you,
>
> Nicole
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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 Tue Sep 30 2014 - 07:30:02 PDT
