“…Using the steepest descent algorithm, the protonation model for each protein structure was energetically stabilized. 4,8,16,17,27,39,40 The equilibration process was performed for each protein structure for at least 1 ns in water at 300 K and 1 atm bar for the NVT and NPT ensembles. The molecular dynamics simulation was run for 25 ns at a constant temperature of 300 K. The Nose-Hoover temperature coupling method was applied for pH ranging from 2.0 to 9.0 (2.0, 3.5, 4.3, 7.4, and 9.0) at various ionic concentrations (10 mM to 50 mM) with a step size of 10 mM each.…”