Figure S5.
Each graph represents the 2D PMF RMSD for a specific sampling window, with the inset plot showing the last 5 nanoseconds of simulation to emphasize convergence. The x-axis of each graph is labeled Window Time in nanoseconds and ranges from 0 to approximately 75 nanoseconds. The y-axis is labeled 2D PMF RMSD in kilocalories per mole and ranges from 0.0 to 3.5 kilocalories per mole. Each graph is numbered from 1 to 21, corresponding to different sampling windows. The inset plots within each graph highlight the convergence of the sampling window over the last 5 nanoseconds. The trends in the graphs show a general decrease in RMSD values over time, indicating convergence. The specific values and trends vary between the different sampling windows, but all graphs demonstrate a similar pattern of convergence.
Convergence criteria for ABF calculations. As specified in the Materials and methods section, convergence of sampling within each independent sampling window was monitored by convergence and plateau of the 2D PMF RMSD. Shown here is the 2D PMF RMSD for each sampling window with the numbers in the inset plot matching the numbers from Fig. S4 C. The inset in each plot shows the last 5 ns of simulation from each sampling window to emphasize the convergence of the sampling window.