. 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 1.

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

Radii Sets	R²_0.25ns	R²_0.5ns	R²_0.75ns	R²_1ns	R²_2ns	R²_3ns	R²_4ns	R²_5ns	R²_6ns
bondi	0.78	0.82	0.83	0.82	0.74	0.61	0.49	0.4	0.36
mbondi	0.71	0.75	0.76	0.77	0.72	0.62	0.54	0.48	0.45
mbondi2	0.79	0.82	0.83	0.82	0.74	0.61	0.49	0.43	0.37
PARSE	0.62	0.67	0.72	0.75	0.77	0.68	0.61	0.53	0.48

R²_n: “R²” stands for coefficient of determination in the MM/PBSA calculation. Here 100, 400, 1200, 2400 MD simulation frames were evenly extracted from one 0.25, 1, 3, 6 ns MD simulation trajectories, respectively.