If Lennard Jones restraints are activated during optimization using
*"env.edat.dynamic_sphere = True"* What does this do exactly?
dynamic_sphere=True is actually the default behavior, which turns on
soft-sphere restraints, not Lennard Jones. For Lennard Jones you would
want to set dynamic_sphere=False and dynamic_lennard=True.
As for what it does, it uses the more correct 6-12 approximation for van
der Waals interactions, rather than a simple harmonic lower bound. Since
this includes a long-range attractive component (soft sphere is just
short-range repulsion) you need a much larger cutoff for your nonbonded
list. The function itself is also more expensive to calculate, so we
don't generally use it for model building. It is used in loop
refinement, however.