Re: [AMBER] Problem related to the RMSD and Atomic fluctuation

From: case <>
Date: Sun, 17 Jul 2011 21:51:40 -0400

On Sun, Jul 17, 2011, Sindrila Dutta banik wrote:
> †
> I want to know what is the difference between the RMSD and atomic
> fluctuation computated by the 'AMBER'. I want to know the mathematical
> equation which is used to compute the two different variables.

The letters "RMS" just mean "root mean square", and the D means "deviation".
People are often very cavilier in using the term "RMSD" without saying what
deviation they are referring to, effectively assuming that it is clear from
context (which is not always true!).

The rmsd command in ptraj starts by finding the translation and rotation
that most closely moves a given snapshot on top of the reference
structure. Then the distance of each atom to the reference structure is
computed, and the root-mean-square of that set of distances is reported as the

The atomic flucutation is a measure of how far a given atom moves from its
average position. This is calculated as the root-mean-square of its distance
from its average position.

Note that atomic fluctuations are a vector: there is one value for each
atom in the protein. The value returned by the rmsd command in ptraj is
a scalar: there is just one value for the entire protein. The atomic
fluctuation, on the other hand, is a property of the entire *trajectory*.
Further, the reference structure for an rmsd command can be anything
you like, whereas the reference structure for calculations of atomic
fluctuations must be the average structure.

> (ii) In my case the protein is composed by¬ four domains. My result
> shows that the RMSD of¬ overall protein¬ is greater than RMSD of all
> individual domains.¬ Is it possible and physically meaningful?¬ ¬

This is a very common result: it is easier to closely superimpose a single
domain onto a reference structure than it is to superimpose four domains.

...hope this helps...dac

AMBER mailing list
Received on Sun Jul 17 2011 - 19:00:03 PDT
Custom Search