[gmx-users] frequence from PCA eigenvalue

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Mon Oct 22 20:37:10 CEST 2007

Dear community,

I have done a principal component analysis on an MD trajectory (g_covar) and
would like to compute the frequency related to the first principle component.
>From what I have read in different sources:

1. the unit of an eigenvalue ei in gromacs (non mass weighted) are : (nm)^(-2)
2. the frequency fi of that principle component (pc) would be : fi = k/sqrt(ei),
where k is a constant with units of velocity.

Are these correct?
What would the value of k be? In my case, I get 43.21 for e1 (first eigenvalue)
and 17 for e2, for a 315 ns trajectory of a 103 residue protein.

I also read that the first pc of a protein simulation often has a high cosine
content, close to 1. In my case the first pc has a cosine content of 0.89. This
pc would thus be related to a diffusive, non-potential related motion, but how
characteristic would it be of my system?

Thank you very much for any info!


Pascal Baillod (PhD student) 
Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	

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