Re: [AMBER] key word to pull out eigenvalues

From: Daniel Roe <>
Date: Tue, 30 Sep 2014 08:14:48 -0600

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,


On Mon, Sep 29, 2014 at 10:37 PM, Nicole Ippolito
<> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Sep 30 2014 - 07:30:02 PDT
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