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

Erik Lindahl lindahl at stanford.edu
Thu Oct 17 21:09:52 CEST 2002

Alan Wilter Sousa da Silva wrote:

>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)?
David and I had slightly different references.

E(A+B) is the total interaction energy inside the A & B groups together. 
That's a sum of
the energy in the A group, the energy in the B group, and the energy 
between them E(AB).

>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?
The E(system) is the sum of


i.e., all possible combinations.

The same goes for any subsystem - the total energy of the subsystem is 
the sum of all possible combinations of it's constituent groups.



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