Warning messages were not issued in this test case. However, in this test case sampling of replicas in individual states was not ideal and the calculations apparently did not fully converge even after 30 ns per window. For this reason all simulations for TrimerTrip were run for 30 ns per window in an attempt to obtain reasonable convergence, though after the fact convergence was only apparent for clip-g1 of TrimerTrip dataset. In addition, an "open" host conformer was extracted from the clip-g11 test simulation trajectory, the guest was docked to the open host conformer, and simulation (found in Docking/GAFF/YANK_REF_2) was re-run in an attempt to allow the host to relax and adapt to the bulky guest. Still longer simulations, or protocol optimizations, might be needed for better converged results.