CHARMM-GUI constant-pH simulator for the constant-pH molecular dynamics simulations

Complex interactions between multiple protonation states at a given pH are overlooked during conventional molecular dynamics (MD) simulation that targets for statistical mechanical ensembles with a fixed composition. Thus, pH sensitive biological systems require a constant-pH MD simulation (CpHMD) that enables variations of protonation states. A few approaches (λ-dynamics, non-equilibrium MD/MC (Monte Carlo), etc) were adopted for CpHMD and implemented in multiple packages including AMBER, CHARMM, GROMACS, and NAMD. In this study, we tested the reproducibility among different theories, implementations, and force fields to find the best practice of CpHMD. We also gauged the performance gap based on the reference pKa quality, and streamlined for optimizing the number of non-equilibrium MD switching steps. We introduced a new CHARMM-GUI module named constant-pH simulator with following features: 1) generating implicit/explicit solvent CpHMD simulation system and input files for various MD packages, 2) providing a site-specific reference pKa for selected titratable residues, and 3) suggesting an optimal set of protein and water force fields for CpHMD simulation. We expect that the benchmarks reported here as well as quick and accurate simulation setup will make constant-pH simulator useful for the community.