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

[R.S.K.Vijayan]

Thanks Micheal for pointing out the mistake

On Fri, Dec 16, 2011 at 4:20 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 performed essential dynamics using  PCA on my system (Protein-DNA
> >complex) considering BB of the protein and the phosphate and sugar of the
> >DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top
> 10
> >principal components are stated below
> >
> >         1 10.1064
> >         2 4.78616
> >         3 4.07406
> >         4 3.48535
> >         5 2.7176
> >         6 2.13348
> >         7 1.75909
> >         8 1.45699
> >         9 1.12932
> >        10 0.893933
> >
> >What i infer from this is that the cumulative variance experienced by  the
> >top 10 PC is  hardly ~ 30 %.
>
> 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 system????
> >b) is it wise to consider the Nucleic acid during essential dynamics or
> >should it be discared and only the Protein BB or CA be considered.
> >
> >Thanking you in advance for your suggestions. My apologies since it sound
> >to be a very general question and rather not very specific to Gromacs.
> >
> >Regards
> >Vijayan.R
>
>
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