[AMBER] atomic fluctuation and average structure

From: Mary Varughese <maryvj1985.gmail.com>
Date: Tue, 10 Sep 2013 06:25:54 +0530

I have some confusion:
on performing atomic fluctuation using ptraj,
the mails suggests an average structure.

but the tutorial says, to get a meaningful average structure, "a mass
weighted backbone rms fit of every frame to the first frame in the
trajectory" should be done.

thus is there two rms?
also is it mass weighted backbone rms fit or just rms first mass :1-20?

thanking you
Mary Varughese
Research Scholar
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Received on Mon Sep 09 2013 - 18:00:03 PDT
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