Computational Biomolecular Chemistry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen D-37077, Germany.
J Comput Chem. 2014 Mar 30;35(8):657-71. doi: 10.1002/jcc.23536. Epub 2014 Feb 5.
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.
我们提出了 Hydrogen Dynamics (HYDYN) 方法，该方法允许在热力学平衡的经典力场分子动力学模拟中明确质子转移。HYDYN 再现了水中过剩质子的特征性质，从特殊对舞蹈到 Eigen 和 Zundel 配合物之间的连续波动，以及第一层溶剂化层之外的水分子重定向。与现有方法相比，HYDYN 的优势在于计算效率、微观可逆性以及易于为任何力场进行参数化。
