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, 20090828 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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