A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

• Autorzy: Weihua Geng
• Języki publikacji: EN

Abstrakty

EN

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

Słowa kluczowe

EN

Electrostatics; Solvated biomolecule; Poisson-Boltzmann equation; Boundary integral equation; Treecode

• Wydawca: De Gruyter Open
• Czasopismo: Molecular Based Mathematical Biology
• Rocznik: 2015
• Tom: 3
• Numer: 1

Daty

otrzymano

2015-02-20

zaakceptowano

2015-05-30

online

2015-07-22

Twórcy

autor

Weihua Geng

• Department of Mathematics, Southern Methodist University, Dallas, TX 75275 USA

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Identyfikatory

DOI

10.1515/mlbmb-2015-0004