AMBER Archive (2005)

Subject: AMBER: RMS fluctuations along modes obtained from PCA

From: Majid moghaddam (erfani_m_at_yahoo.com)
Date: Mon Jan 17 2005 - 07:47:56 CST

Dear AMBER users

I calcaulted RMS fluctuations along the first and the
second modes obtained from PCA by the following
commands:

analyze modes fluct file evec.pev beg 1 end 1 out
rms11
analyze modes fluct file evec.pev beg 2 end 2 out
rms22

May somebody explain me the exact formule by which
these fluctuations are calculated?
The fluctuations along the second mode are greater. I
want to be sure that I have not made any mistakes. I
would appreciate if someone helps me.

Best regards,
M. Moghaddam

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