AMBER: RMS fluctuations along modes obtained from PCA

From: Majid moghaddam <>
Date: Mon, 17 Jan 2005 05:47:56 -0800 (PST)

Dear AMBER users

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

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

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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Received on Mon Jan 17 2005 - 14:52:59 PST
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