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Abstract:
A very efficient scheme is presented to simulate proton transport by classical molecular dynamics simulation coupled with quantum mechanically derived proton hopping. Simulated proton transfer rates and proton diffusion constants for an excess proton in a box of water molecules are in good agreement with experimental data and with previous simulations that employed empirical valence bond (EVB) theory. For the first time, the proton occupancy of an aspartic acid residue in water was computed directly by MD simulations. Locally enhanced sampling or multi copy techniques were used to facilitate proton release in simulations of an imidazole ring in a solvent box. Summarizing, a quasiclassical description of proton transfer dynamics has been able to capture important kinetic and thermodynamic features of these systems at less than 50% computational overhead compared to standard molecular dynamics simulations. The method can be easily generalized to simulate the protonation equilibria of a large number of titratable sites. This should make it an attractive method to study proton transport in large biological systems.
