<p>Hi Michiel,</p>
<p>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.</p>
<p>Cheers,</p>
<p>Tajerk</p>
<p><blockquote type="cite">On Dec 16, 2011 12:07 AM, "Niesen, Michiel" <<a href="mailto:mniesen@coh.org">mniesen@coh.org</a>> wrote:<br><br>>Date: Thu, 15 Dec 2011 15:11:12 -0500<br>
>From: "R.S.K.Vijayan" <<a href="mailto:biovijayan@gmail.com">biovijayan@gmail.com</a>><br>
>Subject: [gmx-users] Eigenvalue values from PCA (a general question)<br>
>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>Message-ID:<br>
> <<a href="mailto:CAMM9PAWRYMQrgzHEriarvOVk7QwuzpfWRm_oWC_0%2BceMeZmwsA@mail.gmail.com">CAMM9PAWRYMQrgzHEriarvOVk7QwuzpfWRm_oWC_0+ceMeZmwsA@mail.gmail.com</a>><br>
>Content-Type: text/plain; charset="iso-8859-1"<br>
<p><font color="#500050">>
>Hi all
>
>I have a query about the eigenvalue values obtained from g_covar and
>g_anaeig
>
>I pe...</font></p><p><font color="#500050">>What i infer from this is that the cumulative variance experienced by the
>top 10 PC is hardly ~ ...</font></p>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.<br>
<p><font color="#500050">
>a) does this imply inadequate sampling by MD or a limited conformational
>change happening in the...</font></p><p><font color="#500050">>b) is it wise to consider the Nucleic acid during essential dynamics or
>should it be discared and ...</font></p><p><font color="#500050">>Thanking you in advance for your suggestions. My apologies since it sound
>to be a very general que...</font></p>---------------------------------------------------------------------<br>
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