Re: [AMBER] atomic fluctuation and average structure

From: Daniel Roe <>
Date: Mon, 9 Sep 2013 20:48:43 -0600


On Mon, Sep 9, 2013 at 6:55 PM, Mary Varughese <> wrote:
> thus is there two rms?

The 'rms' and 'atomicfluct' commands are two different calculations.
RMSD measures the deviation of the coordinates in a target frame to
corresponding coordinates in a reference frame (i.e. how different is
target from reference in Cartesian space), while atomic fluctuations
measure the deviation of those coordinates over all frames. The reason
one typically performs an RMS best-fit prior to calculating an average
structure or atomic fluctuations is to remove overall translational
and rotational motions that will otherwise be present.

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

That's up to you. Typically performing an RMS-fit to an averaged
structure results in less global motion compared to fitting to the
first frame. You could also try rms fitting each frame to the previous
one ('rms previous').


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Sep 09 2013 - 20:00:02 PDT
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