AMBER Archive (2009)

Subject: Re: [AMBER] Regarding principal component analysis using ptraj

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Fri Aug 28 2009 - 06:45:05 CDT

On Fri, 2009-08-28 at 16:34 +0530, Arvind Marathe wrote:
> -----------------------------------------------------------------------
> 1 340.79792
> -0.00620 -0.08939 -0.02576 -0.00649 -0.09078 -0.02791 -0.00449
> -0.08104 -0.03010 0.00057 -0.08734 -0.02879 -0.00762 -0.08015
> -0.03940 -0.00491 -0.06307 -0.02141 -0.00987 -0.06287 -0.01150
> -0.00681 -0.05934 -0.01625 -0.00150 -0.04198 -0.01913 -0.00451
> -0.03329 -0.00936 -0.00017 -0.03949 -0.02144 0.00115 -0.03794
> -----------------------------------------------------------------------
>
> What do the numbers 1 and 340.79792 mean? After the line that gives "1
> 340.79792", there are 325*7 + 5 = 2280 (760*3) fractional values.
> Which of these are eigenvalues, and which are eigenvectors? Are they
> all eigenvalues?

All eigenvalues!? How many of them would you expect!?

As I said, the first number in the first line is simply the number of
the eigenmode/eigenvector. The second number is the eigenvalue itself.
The rest is then obviously the eigenvector.

> Is this output format specified somewhere?

Don't know but you should have all information now to understand the
format.

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