Re: Center of Mass Harmonic Potentials

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
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.

cheers,
   axel.

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

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

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