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

[Niesen, Michiel]

>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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