Figure 3: Comparison of the pK_a’s and pK_a shifts from the GPU single-pH simulations to the CPU replica-exchange simulations or experiment.

The GPU pK_a estimates compared to (a) CPU and (b) experiment and the corresponding plots ((c) and (d)) for the pK_a shifts. The model pK_a’s from Thurlkill et al.⁴¹ were used for calculating the shifts. Data for Asp, Glu, and His resides are colored magenta, dark red, and blue, respectively. The diagonal (y = x) and linear regression lines are colored black and green, respectively. RMSD, regression slope (m) and Pearson’s correlation coefficient (R) are shown. The regression was performed with a zero intercept (R only changed in the second decimal point). In c and d, only pK_a’s with NMR determined pK_a’s are included. In d, the data for Asp26 in thioredoxin are hidden for clarity (the experimental pK_a shift > 4).