For an additive force field, the two numbers are in agreement, E_tot - E_13 - E_23 - E_33 = E_12, by definition. You can easily design a test case that will prove this.

I know. I have it in front of me. ;)
The dielectric constant of the medium is not included in the calculation, at least not explicitly, but its effects are there in the calculation of the forces. GROMACS lets you mess with the relative dielectric via epsilon_r in the .mdp file, but if you do that, you break the force field. All modern force fields and the water models that go along with them assume they are being parametrized relative to vacuum permittivity, as explained by Erik in e.g.:
And that is precisely what I said in my initial post here. However, I suppose I was incorrect when saying that water trajectories would make a difference for what the original topicstarter was asking about energies. There is a difference for what we're trying to do, though, as we do want to see distributions and not energies calculated with an approximate value of epsilon. That whole concept of dielectric constant breaks down for high confinement.


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