[gmx-users] PCA comparison
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...)
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