Figure 6.

Comparison of simulation results according to BDflex and to the 1990 algorithm. (a) Rigid binding pocket. a/R = 0.25; d/R = 0.86. (b) Binding pocket undergoing indifferent switch. The binding pocket switches between an open (with radius a) but non-reactive state and a closed (with radius a^′ = R−d = 0.14R) but reactive state, with ω₊ = ω₋ = 10D/R². The solid and dashed curves are BDflex results using two alternative dividing surfaces (Fig. 1b); symbols are results by the 1990 algorithm. For R²γ/D ≤ 10, the number of trajectories in the BDflex interior simulations is increased tenfold to 40 000, to demonstrate that long simulations for these more challenging cases can be afforded by BDflex. (c) Binding pocket undergoing induced switch. The rates of conformation switch are ω₊ = D/R² and ω₋ = 10D/R² when the ligand is far away but change to ω_I+ = 100D/R² and ω_I− = 10D/R² when the ligand is inside the binding pocket. Correspondingly, $e^{-\beta U_0}$ = 100. The solid curve displays BDflex results using the solid dividing surface in Fig. 1b; symbols are results by the 1990 algorithm.