AMBER Archive (2004)

Subject: Re: AMBER: modes analysis in ptraj

From: David A. Case (
Date: Fri Oct 15 2004 - 10:18:50 CDT

On Thu, Oct 14, 2004, Vlad Cojocaru wrote:

> Could somebody indicate me the way the rms fluct and displacements are
> calculated during modes analysis in ptraj? What do these values
> represent actualy?

Procedures for calculating RMS fluctuations from normal modes are given in
many places. Almost every textbook on physical chemistry should cover this.
You could look in either "Statistical Mechancs" or "Statistical
Thermodynamics", by McQuarrie (kind of a standard, if dated, reference).

> Second, why the rms fluct is calculated along X, Y, Z axes but also a
> general rms is calculated while for the displacement only the displ.
> along X, Y, and Z is given?

The fluctuation is just a direction of the normal mode. Since the amplitude
is not involved, it doesn't make much sense to compute the magnitude of the
vector along the mode direction.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to