From: Giacomo Fiorin (
Date: Fri Dec 08 2017 - 07:16:59 CST

An RMSF is usually computed against the average position of each atom.

On Fri, Dec 8, 2017 at 7:54 AM, Gudrun Gygli <> wrote:

> Hi,
> I am trying to better understand the RMSF command of VMD (Version 1.9.1),
> when used as follows:
> measure rmsf $sel
> where sel is a previously defined selection of atoms in a trajectory.
> The description I could find online (copied in below) does not say which
> structure is used as a reference structure (an average structure/the first
> structure/sth else).
> My guess is that an average structure is calculated and this is used as a
> reference.
> Can anyone help to make this clearer to me?
> *rmsf selection [first first] [last last] [step step]*: Returns the root
> mean square position fluctuation for each selected atom in the selected
> frames. If no first, last, or step values are provided the calculation will
> be done for all frames.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD