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. Author manuscript; available in PMC: 2014 Jan 8.
Published in final edited form as: J Chem Theory Comput. 2012 Dec 12;9(1):153–164. doi: 10.1021/ct300703z

Figure 5.

Figure 5

The QM/MM free energy profile results for HpPNP. Similar to Figure 2, the upper left panel shows the results from all methods with 25 windows. Other panels show the results from individual methods with different numbers of windows: 5 (red), 15 (blue), and 25 (black) windows. For the case of 15 and 5 windows, MBAR fails due to lack of overlap between windows when 75 bins are used (no data in certain bins). While all methods converge with 25 windows, only the VFEP method, with spline (MLE-S) and rational interpolation (MLE-R) functions still gives good results for 5 windows.