Figure : Summary of ABFE predictions using EQ and NEQ methods for each protein-ligand system. NEQ predictions using 600 ps and 2 ns have been included. ∆G prot conf , MUE and RMSE (after adjustment with ∆G prot conf ) and Pearson's r (r p ) are displayed and compared using different methods for all systems. The dashed lines (using the same colour code as bar plots) denote corresponding values for the full dataset. Further details are provided in Table . It is clear that the EQ method is more accurate than the NEQ method. All energies are in kcal/mol. kcal/mol and 0.13-1.33 kcal/mol for EQ and NEQ approaches respectively. Figures 5 (600 ps), S6 and S7 (400 ps to 2 ns) display a direct comparison of results obtained from EQ and NEQ approaches for both raw as well as adjusted data. Given the MUE and RMSE values and looking at the comparison of the raw data, it is clear that the systematic errors in predicted ABFEs have different magnitudes using the two approaches for some systems. Even after adjusting the results using ∆G prot conf for both approaches, the results do not agree too well with MUE and RMSE of 1.59(0.10) and 2.21(0.14) kcal/mol as well as Pearson's r and Spearman's ρ of 0.41(0.06) and 0.43(0.06) respectively (see Figure ). These findings, in conjunction with the fact that EQ results agree better with the experimental values, lead to the conclusion that the EQ approach is preferable over the NEQ approach as it is more accurate and precise. : Correlation plots for absolute binding free energies from the equilibrium (EQ) as well as nonequilibrium (NEQ; 600 ps) alchemical methods against experimental data after adjusting for ∆G prot conf . The solid red line denotes the perfect correlation, whereas the blue, orange and red shaded regions represent ±1, ± 1-2 and ± 2-3 kcal/mol ranges.