Figure 4:

Comparison of the PMF results, and their resulting predicted V111 χ₁ histogram distributions (from 2500 snapshots and with 45 bins between −180° and 180°, the y-axis is the histogram count) along with histogram distributions of real states of alchemical simulations with different protocols. In all cases, V111 is contained in the enhanced sampling SC region for both end states and are contained in both copies of the dual topology. V111₁ and V111₂ indicate the first or second copy of the side chain within the dual topology. Hence for xylene→benzene (XB), at λ=0 the system is represented as xylene in the first copy of the topology that contains V111₁, whereas at λ=1 the system is represented as benzene in the second copy of the topology that contains V111₂. For xylene→0 (X0), at λ=1 the system is in the enhanced sampling “dummy” state such that the apo enzyme is represented by the second copy of the topology that contains V111₂.