[gmx-users] Re: Eigenvalue values from PCA (a general question)

[Niesen, Michiel]

>Hi Michiel,
>
>I disagree, and so does semantics. The cumulative variance of a pc is the
>variance of it plus the sum of the preceding ones. You're talking about the
>cumulative fraction of the total variance.

You are right about the proper word usage. It seemed to me from his question, the use of a % mark when discussing the variance covered by the first 10 PCs, and the conclusions drawn from the value he calculated, that Vijayan meant the cumulative fraction of the total variance. I should name it properly, but I still believe that cumulative fraction of the total variance is the property Vijayan would be interested in.

Regards, 
 Michiel


>
>Cheers,
>
>Tajerk
>
>On Dec 16, 2011 12:07 AM, "Niesen, Michiel" <mniesen at coh.org> wrote:
>
>>Date: Thu, 15 Dec 2011 15:11:12 -0500
>>From: "R.S.K.Vijayan" <biovijayan at gmail.com>
>>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>>To: gmx-users at gromacs.org
>>Message-ID:
>>       <CAMM9PAWRYMQrgzHEriarvOVk7QwuzpfWRm_oWC_0+ceMeZmwsA at mail.gmail.com>
>>Content-Type: text/plain; charset="iso-8859-1"
>
>> >Hi all > >I have a query about the eigenvalue values obtained from
>g_covar and >g_anaeig > >I pe...
>
>>What i infer from this is that the cumulative variance experienced by the
>>top 10 PC is hardly ~ ...
>The cumulative variance described by a set of PCs is not the sum of their
>eigenvalues. You have to take the sum of the first x eigenvalues as a
>percentage of the sum of all eigenvalues to get the cumulative variance.
>
>>a) does this imply inadequate sampling by MD or a limited conformational
>>change happening in the...
>
>>b) is it wise to consider the Nucleic acid during essential dynamics or
>>should it be discared and ...
>
>>Thanking you in advance for your suggestions. My apologies since it sound
>>to be a very general que...

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