AMBER Archive (2004)

Subject: RE: AMBER: what is averaged RMS fluctuation?

From: Thomas E. Cheatham, III (
Date: Mon Jul 12 2004 - 15:28:21 CDT

> I still have one more question. The purpose of this RMS calculation is to
> find out which residue fluctuates most during the MD simulation. So my
> original idea was that: "x axis is the residue number; y axis is RMS
> fluctuation (bigger value means more mobile residue)". And I wanted to
> calculate the fluctuation like this: sqrt(<(r_i(k)-<r_i>)^2>).
> "i" is atom index; "k" is timestep index.
> <r_i> is the averaged position for atom i during simulation.
> r_i(k) is the position for atom i at timestep k.
> I want to know if there is a better way to calculate this. Or is there any
> program can do this kind of calculation (like ptraj)?

This sounds just like what the atomic positional fluctuation (or
B-factors) represent. ptraj ahs a "atomicfluct" command and this can be
by atom or by residue. Large values mean larger fluctuation (from the

When you do the atomicfluct, make sure you RMS fit to a common reference
frame first (ideally the average structure but the first frame is likely
OK too).

Good luck.

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