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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The message from all your analysis is very clear:<br></div>Your principal components have not converged.<br><br>Berk.<br><br><hr id="stopSpelling">> Date: Thu, 23 Oct 2008 14:37:00 +0000<br>> From: rcsqtc@iiqab.csic.es<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] PCA comparison<br>> <br>> <br>> Hi Berk,<br>> Indeed, when I say that the overlap is below 0.4 I mean the highest<br>> values of the matrix of inner products. I expected the vectors to be<br>> quite similar with their neighbours, i.e. I expected vector 5 to have a<br>> high inner product with 5, or 4 or 6 of the other set. But this diagonal<br>> trend, although present, is very weak, and is in fact more present for<br>> the lower pc that the higher!<br>> A part from the cosine content, we have checked the projections of the<br>> trajectory, and except for the 1st and 2nd pc's, the other exhaustively<br>> oscillate around the mean value, which I though indicated good sampling.<br>> Otherwise, how can I asses if the PCA makes any sense? (there are papers<br>> that do PCA with shorter trajectories...)<br>> Thanks!<br>> Ramon<br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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