RE: AMBER: what is averaged RMS fluctuation?

From: Ross Walker <>
Date: Mon, 12 Jul 2004 11:51:47 -0700

> Sorry to ask about such a trival question. What is the
> definition of the RMS fluctuation averaged over a period of time?

This depends on exactly what you mean. E.g you can calculate a root mean
square displacement for the difference between a structure at time t=0 and a
structure at time t=t1. This will give you the RMSD between these two
structures. This is an rmsd but is it an average? You could also calculate
the rmsd at a series of times t1, t2... And then average these to get an
average rmsd over time but I'm not sure what you'd learn from this.

A better idea would be to plot the rmsd to the initial structure as a
function of time, the number of samples obviously depending on how often you
wrote to the mdcrd file. You could do this individually for each residue and
it may give you some kind of feel for the fluctuation of each with respect
to the initial structure. Ptraj will do this for you. See the tutorials for
info on how to calculate structural rmsd's.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Jul 12 2004 - 19:53:00 PDT
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