[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
E(protein-protein)
E(protein-ligand)
E(protein-sol)
E(protein-ion)
E(ligand-ligand)
E(ligand-sol)
E(ligand-ion)
E(sol-sol)
E(sol-ion)
E(ion-ion)
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.
Cheers,
Erik
More information about the gromacs.org_gmx-users
mailing list