Re: [AMBER] Regarding principal component analysis using ptraj

From: Arvind Marathe <bahuroopi.gmail.com>
Date: Fri, 28 Aug 2009 12:56:53 +0100

On Fri, Aug 28, 2009 at 5:15 PM, Hannes
Loeffler<hannes.loeffler.stfc.ac.uk> wrote:
> 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.

ohkk - that means the default value for the 'vecs' flag for the
'analyze' command is 1. I was under the impression that by default, it
gives all the eigenvectors and eigenvalues in descending order of
eigenvalues - hence my confusion.

>>  Is this output format specified somewhere?
>
> Don't know but you should have all information now to understand the
> format.

Yes - thanks a lot.

Regards,
arvind

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Received on Wed Sep 02 2009 - 23:05:58 PDT
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