# AMBER Archive (2009)Subject: RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sun Aug 02 2009 - 22:47:07 CDT

Dear Hannes,

Thank you. The problem has been solved.

Best regards,

Cat

> Subject: RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule.
> From: hannes.loeffler_at_stfc.ac.uk
> To: amber_at_ambermd.org
> Date: Fri, 31 Jul 2009 08:27:54 +0100
>
> Ok, I see that you don't really understand what you are doing.
>
> The '*' mask means ALL atoms. Unless this selection is not just the
> molecule(s) you are interested in you are obviously trying to fix the
> wrong part of your system. So make sure that you use here the same mask
> as in the 'matrix' command.
>
> Why simulation length matters? PCA is a statistical method as you are
> calculating the variance-covariance matrix as an _average over time_.
> This should make it clear to you that you will need sufficient sampling
> before you can rely on your results.
>
> Here are two sample input files for computing the
> eigenvectors/eigenmodes and the projection of the eigenvectors onto the
> trajectory for a protein with 100 residues. The examples are just meant
> to guide you. So adapt it to your problem.
>
> -------------------------- PCA.in ------------------------
> rms first :1-100_at_CA
>
> # PCA analysis
> matrix covar name PCA :1-100_at_CA
> analyze matrix PCA vecs 25 out evec.pev
> -------------------------- PCA.in ------------------------
>
> -------------------------- proj.in ------------------------
> # centering and imaging not necessary if selection is just one molecule
> center :1-100 mass origin
> image origin center
>
> rms first :1-100_at_CA
>
> projection :1-100_at_CA modes evec.pev out proj.ppj beg 1 end 25
> -------------------------- proj.in ------------------------
>
>
> Hope that helps,
> Hannes.
>
>
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