A boundary integral Poisson-Boltzmannsolvers package for solvated bimolecularsimulations

Molecular Based Mathematical Biology

卷:3

Geng Weihua¹ 

[1] Department of Mathematics, Southern Methodist University, Dallas, TX 75275 USA;

关键词: Electrostatics;    Solvated biomolecule;    Poisson-Boltzmann equation;    Boundary integral equation;    Treecode;   

DOI  :  10.1515/mlbmb-2015-0004

来源: DOAJ

【 摘 要 】

Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existenceof the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostaticfield, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmannequation can circumvent these numerical challenges and meanwhile conveniently use the fast numericalalgorithms and the latest high performance computers to achieve combined improvement on both efficiencyand accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solversin pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features andfunctions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitativelyreport the solvation free energy computation of these boundary integral PB solvers benchmarked withMatched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite differencePoisson-Boltzmann solver.

【 授权许可】

Unknown