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PCA refers to covariance analysis (though SVD gives the same results).<br>Principal components are obtained by projecting the trajectory onto<br> the eigenvectors of the covariance matrix.<br>I just wanted to know why the option -ref was offered and if it had any significance.<br>Thanks<br>Vijaya<br><br>> Date: Thu, 18 Mar 2010 17:51:04 +0100<br>> Subject: Re: [gmx-users] g_covar -ref<br>> From: tsjerkw@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hi Vijaya,<br>> <br>> Well, to start with that will be something as calculating the<br>> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith<br>> atom of the conformation x and the reference structure r and the sum<br>> is over time/observations. In the case of no variation in xi, the<br>> value you get will still be finite, in stead of zero, as would<br>> probably be most meaningful.<br>> Now for the covariances, there's a bit more to it. The covariance is<br>> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When<br>> there is no correlation, the deviations about the mean are random and<br>> average out to zero. But with the deviations against a reference, that<br>> is not the case. So the results should be regarded meaningless, unless<br>> you have a good reason for doing so, and come with a solid<br>> justification. Okay, there may be a purpose, but I'll leave that to<br>> your imagination :)<br>> <br>> Hope it helps,<br>> <br>> Tsjerk<br>> <br>> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian<br>> <vijaya65@hotmail.com> wrote:<br>> > Hi<br>> > Has anyone studied the effect of using different reference structures,<br>> > not the average structure, when carrying out PCA. Does it make sense to use<br>> > a structure besides the average to calculate the covariance matrix?<br>> > Thanks<br>> > Vijaya<br>> ><br>> ><br>> ><br>> > ________________________________<br>> > Hotmail: Trusted email with powerful SPAM protection. Sign up now.<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> <br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> Groningen Institute for Biomolecular Research and Biotechnology<br>> University of Groningen<br>> The Netherlands<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='http://clk.atdmt.com/GBL/go/210850552/direct/01/' target='_new'>Sign up now.</a></body>
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