PBCAVE: Program for exact classification of the mesh points of a protein with possible internal cavities and its application to Poisson–Boltzmann equation solution

The main contribution of the program is in the analytic approach to the setting of dielectric constant for all discretization points of a grid in the computational domain according to their locations with respect to the molecular surface allowing also taking into account possible cavities. Assigned values of dielectric constant are used in a solver of the linear Poisson–Boltzmann equation for a protein–water system using a finite difference method.

该程序的主要贡献在于对计算域内网格所有离散化点介电常数的分析设定方法，该方法根据各离散化点相对于分子表面的位置进行设定，同时亦允许考虑可能存在的空腔。所赋予的介电常数值被应用于求解蛋白质-水系统线性泊松-玻尔兹曼方程的求解器中，采用有限差分法进行计算。