Re: [AMBER] Question regarding COM and atom pulling

From: Jason Swails <>
Date: Tue, 9 Oct 2012 21:54:09 +0200

On Tue, Oct 9, 2012 at 7:11 PM, Fabrício Bracht <> wrote:

> If, hypothetically, one was to calculate the binding free energy
> between two structures, (say two alpha helices or a ligand in its
> binding pocket), and for this, specified an atom in both structures to
> do the pulling, would this have the same effect as if the pulling was
> done using the center of mass? What I mean is, if I calculated the
> center of mass of structure A (hypothetical structure A) and luckily
> the COM of this structure coincides to atom number ## . If I applied
> the force using the COM formalism be the same as specifying that this
> structure should be pulled with the spring attached to this atom?

Formally I think the answer should be "no". When defined as the COM or COG
(center of geometry), I think the forces calculated from the restraints are
(and should be) distributed throughout all atoms involved in the COM via
the chain rule.

When a single atom is defined, obviously the entire force is applied to
that one atom.

If the system was completely rigid, this would be equivalent (since the net
force on the rigid object would be the same). Since biological systems are
flexible, though, I think there is a difference.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Oct 09 2012 - 13:00:05 PDT
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