Table 6.

Effect of changing protonation states in molecular dynamics simulations

Protonation state	Avg. RMSD	Avg. pKa GLU 35 (std. dev.)	Avg. pKa ASP 52 (std. dev.)	pKa GLU 35 avg. titr. curv.	pKa ASP 52 avg. titr. curv.
35 Glu-, 52 Asp-	0.95	3.60 (0.64)	2.88 (0.68)	3.70	2.90
35 GluH, 52 Asp-	0.86	5.29 (0.47)	3.37 (0.50)	5.40	3.40
35 Glu-, 52 AspH	1.19	2.84 (0.59)	4.90 (0.57)	2.90	5.00
35 GluH, 52 AspH	0.94	4.75 (0.88)	4.86 (0.85)	4.70	5.00

Avg. RMSD: The average RMSD between calculated and experimentally measured pKa values for all groups.