Daniel Russel wrote: >> For EM we solved this years ago with a scaling factor. Ideally the scale >> would simply be N^2 where N is the number of particles in the system. > Why quadratic rather than linear?
Most physics-based scores are interaction energies between pairs of particles. But not all of course, otherwise this would be a solved problem already.
> I don't see that being able to minimize the score cares about whether it > increases as you add atoms
That's not my point. The point is that physics-based forcefields are balanced that way (and making up a new forcefield is a decades-long endeavor). Rescaling all the terms is not likely to give correct behavior. I'm not talking about Grand Canonical type approaches here, although they should certainly be considered too.
> A key invariant is that changing the resolution of the representation > should not change things too much.
That certainly makes sense.
Ben