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
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle