Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
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CPB的特点：使用自适应笛卡尔网格的泊松-玻尔兹曼求解器。
DOI：
10.1002/jcc.23791
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发表时间：
2015
影响因子：
3
通讯作者：
Boschitsch,AlexanderH
中科院分区：
文献类型：
--
作者：
Fenley,MarciaO;Harris,RobertC;Mackoy,Travis;Boschitsch,AlexanderH
演示了基于自适应笛卡尔网格（ACG）的泊松-玻尔兹曼（PB）求解器（CPB）的功能。CPB使用ACG求解各种PB方程，ACG是根据计算域的分层八叉树分解构建的。该过程减少了所需的点数，从而减少了计算需求。在分子内部，CPB求解静电势（Eq）的反应场分量（Eq rf），消除Eq中的电荷诱导奇点。CPB还可以使用最小二乘重建方法来改善分子表面的电导率估计。所有曲面（包括排除溶剂的曲面、高斯曲面等）都是通过分析创建的，从而消除了与三角化曲面相关的错误。这些功能允许CPB产生详细的表面映射的极性和计算极性溶剂化和结合自由能的大型生物分子组件，如核糖体和病毒，减少计算需求相比，其他泊松-玻尔兹曼方程求解器。读者可参考http：//www.continuum <$dynamics.com/solution <$mm.html了解如何获得CPB软件。© 2014 Wiley Periodicals，Inc.
The capabilities of an adaptive Cartesian grid (ACG)‐based Poisson–Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction‐field component (ϕrf) of the electrostatic potential (ϕ), eliminating the charge‐induced singularities inϕ. CPB can also use a least‐squares reconstruction method to improve estimates ofϕat the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps ofϕand compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson–Boltzmann equation solvers. The reader is referred to http://www.continuum‐dynamics.com/solution‐mm.html for how to obtain the CPB software. © 2014 Wiley Periodicals, Inc.