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Boxplots of the smallest RMSDs for 10 trials of (a) Chignolin folding (3000 iterations) and (b) Trp-cage folding (4000 iterations) for each method: PaCS-MD, TS-MD with α = 1.01, 1.05 and C = 0.05, and TS-MD without penalty with C = 0.01, 0.03, 0.05, 0.1, 0.2.
