AMBER Archive (2009)

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

From: Hannes Loeffler (
Date: Fri Aug 28 2009 - 02:28:29 CDT

On Fri, 2009-08-28 at 12:24 +0530, Arvind Marathe wrote:
> However, it contains a 760*3 x 760*3
> matrix. Why are the hydrogen atoms not getting excluded? Is something
> wrong with the ptraj input file?

Use the mask for the 'matrix' command.

> The second question is regarding the file eigen_vectors.dat. Shouldn't
> the eigen_vectors.dat file also have a 760*3 x 760*3 matrix if the
> cov_mat is 760*3 x 760*3? I am getting a matrix of 654 * 7 in the
> eigen_vectors.dat file. The two header lines give:
> -----------------------------------------------------------------------
> Eigenvector file: COVAR
> 2280 2280
> -----------------------------------------------------------------------
> I assume the input matrix is being read correctly. So why am i getting
> this size of 654 * 7?

2280/3 = 760. You didn't get a matrix of '654 * 7'. This is just an
arbitrary output format.

> Finally, how do i get the eigenvalues themselves? Does one of the 7
> columns in the file eigen_vectors.dat give the eigenvalues? But if
> that is the case, shouldn't they be in descending order? None of the
> columns in that file are in descending order.

Ok, the output format is as follows:
First line is just a title line
Second line gives the size of the matrix
The following lines up to ' ****' is the average structure.
All following entries between ' ****'s are the running number and actual
value of the eigenvalue (neatly in descending order) first line followed
by the corresponding eigenvector.

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