[gmx-users] Editing index.ndx, Ener. Groups and rerun

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Thu Oct 17 19:55:42 CEST 2002

On 17 Oct 2002, David wrote:
> No you can not. You can however sum the terms after wards:
> E(A+B) = E(A) + E(B) + E(AB) is the interaction energy
> where E

where E...? Actually, what'd be E(AB) and E(A+B)?

On 17 Oct 2002, Erik wrote:
>It's still easy to solve your problem, though. Assume you have four
>energy groups: Protein, HEME, SOL, IONS. If you want to know the energy
>between Protein+HEME and SOL/ION, just run g_energy and add the energy
>of the combinations Protein-SOL and HEME-SOL (or ION). There's even a
>-sum option that does it for you :-)

	I can know E(Protein), E(Ligand), E(SOL) and E(ION), however I
think E(System) is not equal to the direct sum of the partial energies.
To simplify, I just want a rude evaluation for energy of interaction of
the complex Protein/Ligand, i.e. E(Protein/Ligand).

	So, could you both, please, clarify me a little bit more?

I beg your pardon if I'm being fool.


Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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