AMBER Archive (2009)

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

From: Arvind Marathe (bahuroopi_at_gmail.com)
Date: Fri Aug 28 2009 - 06:04:22 CDT

On Fri, Aug 28, 2009 at 12:58 PM, Hannes
Loeffler<hannes.loeffler_at_stfc.ac.uk> wrote:
> 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.

Fine. Will try that and get back if there is a problem. But i am still
curious as to what was wrong with the ptraj input where i instructed
it to strip the hydrogens.

>> 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.

Sorry, i had initially checked only the first and the last few lines.
But i still do not understand the output after the ****s. Following
are the first few lines after the coordinates of the average structure
and the ****s:

-----------------------------------------------------------------------
    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? Is this output format specified somewhere?

Thanks for your help.

Regards,
arvind

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