AMBER Archive (2004)

Subject: AMBER: what is averaged RMS fluctuation?

From: jz7_at_duke.edu
Date: Mon Jul 12 2004 - 11:17:30 CDT

Dear all,

Sorry to ask about such a trival question. What is the definition of the
RMS fluctuation averaged over a period of time? For example, I have a
trajectory of the MD simulation. I want to know the fluctuation of each
residue during the MD simulation. What is the best way to describe it
(something like a RMSD plot?)?

Thanks a lot!
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