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. Author manuscript; available in PMC: 2018 Oct 10.
Published in final edited form as: J Chem Theory Comput. 2017 Sep 28;13(10):4660–4674. doi: 10.1021/acs.jctc.7b00651

Figure 5.

Figure 5

Population percentage of the configurations in the DOWN macrostates and probability density of binding energy at the λ = 1.0 state. The red line is the benchmark — the BEDAM (replica exchange simulation) results. (a) Comparison of the population percentages of the configurations in the DOWN macrostate estimated by Conventional UWHAM, Stratified-UWHAM, Stratified RE-SWHAM (based on the raw data generated by two sets of 72 ns independent MD simulations) and the benchmark. The blue stars are the Stratified-UWHAM estimates when the data at the largest seven λ-states are clustered into UP and DOWN macrostates. The black circles are the Stratified RE-SWHAM estimates; and the black line with dots are the conventional UWHAM estimates when the data at the unconverged λ-states are simply combined as the input of that λ-state. (b) the probability density of binding energy at the λ = 1.0 state obtained by replica exchange simulations. The blue line is the probability density of binding energy of the configurations in the UP macrostate; the green line is the probability density of binding energy of the configurations in the DOWN macrostate; and the red line is the overall probability density of binding energy at the λ = 1.0 state. (c) Comparison of the probability density of binding energy at the λ = 1.0 state estimated by conventional UWHAM to the 32 independent simulations and the benchmark. The bars show the UWHAM estimates. (d) Comparison of the probability density of binding energy at the λ = 1.0 state estimated by Stratified-UWHAM, Stratified RE-SWHAM and benchmark. The blue dots are the Stratified-UWHAM estimates. The bars are the Stratified RE-SWHAM estimates. As can be seen by comparing the four figures, only the Stratified-UWHAM and Stratified RE-SWHAM estimates agree with the benchmark.