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Figure 10 | BMC Bioinformatics

Figure 10

From: A replica exchange Monte Carlo algorithm for protein folding in the HP model

Figure 10

Effect of number of local steps on run-time. Results for mean runtimes of 100 independent runs using different numbers of local steps during Monte Carlo search, ranging from 5 to 5000, are presented. The value of local steps is plotted in log scale. Results in 2D for folding S1-7 are shown on the left and those of folding S2-7 in 3D are shown on the right. The relationship in this instance appears to be more erratic, with poorest performance often observed at the extreme values tested. The default value of 500 local steps reports good relative running times for both REMC m and REMC pm in both 2D and 3D.

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