基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.

Calculations of Free Energies Based on the Combination of Molecular Dynamics Simulations and Continuum Solvation Model

In recent years, the methods of calculating free energies based on the combination of molecular dynamics simulations and continuum solvation models have drawn more and more attention, in which MM/PBSA is the most representational one. In MM/PBSA, the sum of molecular mechanical energies of the molecules is calculated from molecular mechanics (MM); the polar solvation energy in continuum solvent is usually computed using a finite-difference Poisson-Boltzmann (PB) model; and the nonpolar solvation energy is often obtained from the solvent-accessible surface area (SA). In this paper, the progress and application of MM/PBSA, as well as some research works in our group, are introduced.