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

[Tsjerk Wassenaar]

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.

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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