Re: Center of Mass Harmonic Potentials

From: Axel Kohlmeyer (
Date: Mon Jan 18 2010 - 19:33:18 CST

On Mon, 2010-01-18 at 18:59 -0600, Keith Battle wrote:
> Hi NAMD users,

hi keith,

> 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.

it is quite easy for center of mass restraints as well. ;)

the force vector on the individual atoms is the force vector
on the center of mass scaled by the mass fraction of the
individual atom in the molecule or group.


> Best,
> Keith Battle
> Research Assistant
> Department of Chemistry
> University of South Alabama
> 251-214-6877

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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