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. Author manuscript; available in PMC: 2018 Jun 13.
Published in final edited form as: J Chem Theory Comput. 2017 May 1;13(6):2930–2944. doi: 10.1021/acs.jctc.6b01183

Figure 4. Convergence of AlGDock calculations.

Figure 4

The standard deviation of free energy estimates as a function of the number of replica exchange cycles, for (a) changing the ligand temperature from 300 K to 600 K, and (b) scaling the receptor-ligand interaction grid from 0 to 1 while decreasing the temperature. Values were calculated between dipropyl disulfide, thianaphthene, isobutylbenzene, dibutyl-disulfide, phenylacetylene, cyclohexane, 1-heptanol, 1-propanol, 1,1-diethylurea, p-xylene, and a snapshot of T4 lysozyme from an alchemical pathway calculation with n-hexylbenzene. The thick black line is the average of the standard deviation across the 10 complexes.