Re: rmsd calculation in namd

From: Niklaus Johner (
Date: Fri Sep 07 2012 - 15:53:16 CDT


You can use the PLUMED plugin to do this ( But to do so you'll have to recompile namd with the plugin.



Niklaus Johner
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065

On Sep 7, 2012, at 3:57 PM, Guanglei Cui wrote:

Hi everyone,

can someone let me know if it's possible to define the rmsd collective
variable such that the overlay and rmsd calculation are done on
separate sets of atoms? Thanks very much.


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