Subject: mass-weighted RMS

From: <[email-masked]>
Date: Tue, 26 Mar 1996 11:08:14 -0800 (PST)

I am interested in people's opinions on use of RMS comparisons
of different conformations of the same molecule. To my mind,
the mass-weighted approach is more appropriate than the
unweighted, geometric approach. I.e. mass-weighted:

 RMS = sqrt( (d1^2 * mass1  +  d2^2 * mass2  +  d3^2 * mass3 ...) / total_mass)

as opposed to geometric:

 RMS = sqrt(d1^2 + d2^2 + d3^2 ...) 

where 'd1' is the distance between the positions of atom 1 
in 2 conformers. 

The rationale for 'preferring' heavier atoms is that they
are less mobile (it takes more energy to get them moving
at a given velocity) and therefore more indicative of 
structure. Is there any situation where mass-weighting
would not be desirable? 

This issue arose when someone compared the results of
my trajectory analysis program, Carnal (part of AMBER), 
with RMS measurements obtained using another program 
package, which does not do mass weighting.

Bill Ross