. Author manuscript; available in PMC: 2016 Sep 30.

Published in final edited form as: J Comput Chem. 2015 Jul 27;36(25):1859–1873. doi: 10.1002/jcc.24011

Table 8.

The coefficient of determination of Experimental and Predicted Binding Free Energies of Different Multiple MD Trajectory Lengths and Radii Sets in MM/PBSA Calculations.

Radii Sets	R²_0.25n	R²_0.5ns	R²_0.75	R²_1ns
bondi	0.77	0.73	0.73	0.75
mbondi	0.76	0.74	0.74	0.76
mbondi2	0.77	0.73	0.73	0.76
PARSE	0.6	0.59	0.61	0.65

^a R²_n: “R²” stands for coefficient of determination in the MM/PBSA calculation. Here 600, 1200, 1800, 2400 MD simulation frames were evenly extracted from six 0.25, 0.5, 0.75, 1 ns MD simulation trajectories, respectively.