From: Chris Harrison (charris5_at_gmail.com)
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 <
> 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?
-- 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 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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