Re: RMSD collective variable - Different atons to align and to calculate RMSD

From: Chris Harrison (
Date: Thu Feb 02 2012 - 13:54:55 CST

The are the same. It is not clear to me why you'd want to calc the RMSD of
a set of atoms which do not correspond to the subset used for alignment.
 The resulting measurement (RMSD) would be erroneous. Can you elaborate
why you'd want this feature available?


On Thu, Feb 2, 2012 at 12:19 PM, Paulo Cesar Telles de Souza <> wrote:

> Dear colleagues
> I'm trying to use the ABF method to get the free energy difference
> between two conformation states of a protein. For this, I tried to use
> as a reaction coordinate the RMSD of these two conformations, so that
> I get a 2D graph (RMSD conformation 1 x RMSD conformation 2, with the
> free energy differences given by a color scale). However I have a
> question regarding the use of RMSD as a collective variable in the
> NAMD program: Can I specify, in the RMSD collective variable,
> different atoms for the alignment of protein and to calculate the RMSD
> itself. Or must they necessarily be the same in the NAM program?
> Thanks
> Paulo

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 773-570-6078                Fax: 217-244-6078

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