Merge pull request #1083 from RosettaCommons/dougrenfrew/mm_lj_memory_issues
This PR fixes an issue with the MM LJ term where is was creating a full neighbor list rather than residue neighbor lists during minimization requiring more than 20GB of memory to minimize a protein. Also includes a non-compiled pilot app, some updates to the MM torsion params for small solvent molecules, and the conversion of some std::cout statements to tracers.
The cyclization, doug_dock_design_min_mod2_cal_cal, oop_dock_design, and make_rot_lib tests show show expected differences in output since they all minimize with mm_std