AMBER Archive (2004)

Subject: Re: AMBER: intramolecular energies

From: David A. Case (
Date: Tue Sep 28 2004 - 10:43:11 CDT

On Mon, Sep 27, 2004, Guanglei Cui wrote:

> Sorry, I mistyped it. It should be intermolecular, not intramolecular.
> Anal doesn't seem to have PME. I guess I could calculate intra first and
> subtract it from the total energy calculated with PME to get the
> intermolecular energies. Is this correct?

I guess this depends on what you mean by intermolecular energies, i.e. what
do you really want? PME energies are not pairwise decomposable in the way
that conventional force fields are. If you want the interaction energy
between two specific molecules, anal could do that for you. But since the
reciprocal part of the energy includes both "inter" and "intra" components,
it's not clear how such a division would be made (or what use it would be
in the first place...)


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