How to remove center of mass translation of macromolecule

From: Teerapong Pirojsirikul (
Date: Wed Jun 12 2013 - 03:05:36 CDT

Hi NAMD users,

I have been looking for how to remove center of mass translation of a
macromolecule. I have read many threads regarding this issue in the mailing
list but still got confused. I'm working on a sampling problem and want to
reconstruct a free energy surface as a function of Cartesian coordinates
(x,y, and z) of a certain ion moving in an active site of an RNA molecule.
As a result, I need to perform the MD simulation at a fix orientation (by
removing rotation and translation of the RNA). I can successfully fix the
rotation by blocking the backbone of the molecule using orientation colvar
module. But I'm wondering what is the easiest way to remove the translation
of the RNA. I have tried fixing one atom but am curious whether this will
cause any artificial dynamics to my system or to the fixed atom. Also I
have seen many people talking about dummy atom but don't quite have a clear
idea how to make use of it. Any advice would be appreciated.


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