  We investigate the role of order/disorder transitions in alchemical
simulations of protein-ligand absolute binding free energies. We show, in the
context of a potential of mean force description, that for a benchmarking
system (the complex between the L99A mutant of T4 lysozyme and 3-iodotoluene)
and for a more challenging system relevant for medicinal applications (the
complex of the farnesoid X receptor and inhibitor 26 from a recent D3R
challenge) that order/disorder transitions can significantly hamper Hamiltonian
replica exchange sampling efficiency and slow down the rate of equilibration of
binding free energy estimates. We further show that our analytical model of
alchemical binding combined with the formalism developed by Straub et al. for
the treatment of order/disorder transitions of molecular systems can be
successfully employed to analyze the transitions and help design alchemical
schedules and soft-core functions that avoid or reduce the adverse effects of
rare binding/unbinding transitions. The results of this work pave the way for
the application of these techniques to the alchemical estimation with explicit
solvation of hydration free energies and absolute binding free energies of
systems undergoing order/disorder transitions.
