Center of Mass Harmonic Potentials

From: Keith Battle (
Date: Mon Jan 18 2010 - 18:59:25 CST

Hi NAMD users,


Our group has been performing potential of mean force calculations using a
variety of techniques for some time now. Our systems are rather large so we
use center of mass harmonic potentials to define the desired reaction
coordinate. Our results have been encouraging, but we have never fully been
able to understand how the force applied by the harmonic potential is
distributed between atoms in a molecule during a free energy calculation.
It's quite easy to understand the concept when applied between two atoms of
a molecule, but not so easy to understand when the force is applied to the
center of mass. Any insight would be appreciated.





Keith Battle

Research Assistant

Department of Chemistry

University of South Alabama



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