[gmx-users] PCA comparison

Berk Hess gmx3 at hotmail.com
Thu Oct 23 17:23:23 CEST 2008


The message from all your analysis is very clear:
Your principal components have not converged.


> Date: Thu, 23 Oct 2008 14:37:00 +0000
> From: rcsqtc at iiqab.csic.es
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PCA comparison
> Hi Berk,
> Indeed, when I say that the overlap is below 0.4 I mean the highest
> values of the matrix of inner products. I expected the vectors to be
> quite similar with their neighbours, i.e. I expected vector 5 to have a
> high inner product with 5, or 4 or 6 of the other set. But this diagonal
> trend, although present, is very weak, and is in fact more present for
> the lower pc that the higher!
> A part from the cosine content, we have checked the projections  of the
> trajectory, and except for the 1st and 2nd pc's, the other exhaustively
> oscillate around the mean value, which I though indicated good sampling.
> Otherwise, how can I asses if the PCA makes any sense? (there are papers
> that do PCA with shorter trajectories...)
> Thanks!
> Ramon
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081023/9e9ccbc8/attachment.html>

More information about the gromacs.org_gmx-users mailing list