Explicit proton transfer in classical molecular dynamics simulations.
We present Hydrogen Dynamics (HYDYN), a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, from the special pair dance, to the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the first solvation layer. Advantages of HYDYN with respect to existing methods are computational efficiency, microscopic reversibility, and easy parameterization for any force field.
Computational Biomolecular Chemistry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen D-37077, Germany.
Maarten G
MG
Wolf
Gerrit
G
Groenhof
D056004:Molecular Dynamics Simulation; D011522:Protons; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D011522:Protons; D014867:Water
MC; excess proton; force field; molecular dynamics; proton transfer; λ-dynamics