[gmx-users] Essential dynamics and cosine content

Leonardo Giantini Trabuco ltrabuco at cecm.usp.br
Tue Jun 29 21:50:11 CEST 2004

Dear gmx-users,

I'm performing some essential dynamics analysis. My first principal
component happened to have a large cosine content (0.807317), which
indicates it is related with random diffusion.

I'd like to ask you if there is some threshold of cosine content, above
which we consider de principal component to be related with random

So now I'm not very sure of what principal components I should take
into account. Is it ok to simply ignore the first principal component
and analyze, for instance, the second and the third? 

And how do I know that I'm analyzing a sufficient ammount of principal
components? That should have something to do with the relative
positional fluctuation but, again, I dont't know which threshold I
should use. 

Thank you very much in advance!


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