Improve exception handling for protein mutations

[ijpulidos]

Recently we have noticed that handling nonbonded exceptions have been getting a little too slow for protein mutations, probably due to the fact that now are alchemical unit can be pretty big (since it's the whole protein). Maybe there's a better way to deal with this, but for now we are just iterating over all the bonds/atoms and handling the exceptions on all of them.

To do that we are just manually getting the forces exceptions and adding/removing/rescaling(1-4s) accordingly. I wonder if instead of doing this manually we could rely more on the createExceptionsFromBonds() method for the NonBondedForce to improve the performance when handling exceptions.

Note that this probably won't improve things much for protein-ligand systems.

Originally posted by @ijpulidos in #105

[ijpulidos]

There are new improvements on this that claim maybe no handling of exceptions could be possible. Relevant literature in https://arxiv.org/abs/2504.14398