You use the chain rule and multiply the derivative with respect to the
distane by the derivative of the COM wrt the atom positions.
On Jan 18, 2010, at 7:56 PM, "Keith Battle" <keith.battle.gmail.com>
wrote:
> Hi AMBER 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.
>
>
>
> Best,
>
>
>
>
>
> Keith Battle
>
> Research Assistant
>
> Department of Chemistry
>
> University of South Alabama
>
> 251-214-6877
>
>
>
>
>
>
>
>
>
>
>
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Received on Mon Jan 18 2010 - 18:00:02 PST
