AMBER Archive (2006)

Subject: AMBER: PCA analysis

From: Jardas sucuriba (jarda_s_at_hotmail.com)
Date: Wed Dec 27 2006 - 23:04:41 CST

Hi

I am interested in getting a graph of the fluctuations versus mode number. I
calcaulted RMS fluctuations along five modes obtained from PCA using the
following
commands:

trajin mds.mdcrd
rms first @CA
matrix covar name mcovar @CA out mcovar.dat
analyse matrix mcovar out evec.pev name evecs vecs 5
analyze modes fluct stack evecs out analizeprojCA1.ppj beg 1 end 1
analyze modes fluct stack evecs out analizeprojCA2.ppj beg 2 end 2
analyze modes fluct stack evecs out analizeprojCA3.ppj beg 3 end 3
analyze modes fluct stack evecs out analizeprojCA4.ppj beg 4 end 4
analyze modes fluct stack evecs out analizeprojCA5.ppj beg 5 end 5

However, the fluctuations increase along the modes. For instance, the total
fluctuation along the first mode is 31,981 while for the fifth mode is
172.828. I think this is wrong...Does anyone knows why is this happening? Is
there something wrong with my script?

Best regards
Jardas

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