From: Gudrun Gygli (
Date: Fri Dec 08 2017 - 06:54:33 CST


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.