AFMPB

AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. It is described an adaptive fast multipole Poisson-Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast multipole method with the Krylov subspace methods, which are applied to solve a well-conditioned boundary integral equation of the linearized Poisson-Boltzmann equation. Numerical experiments show the efficiency of the method in the framework of relatively large molecules on current desktop computers.


References in zbMATH (referenced in 9 articles )

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  1. Wu, Hao; Ying, Jinyong; Zou, Qingsong: Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent (2021)
  2. Li, Jiao; Ying, Jinyong; Lu, Benzhuo: A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule (2019)
  3. Quan, Chaoyu; Stamm, Benjamin; Maday, Yvon: A domain decomposition method for the Poisson-Boltzmann solvation models (2019)
  4. Xie, Dexuan: New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation (2017)
  5. Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo: Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy (2015)
  6. Geng, Weihua; Krasny, Robert: A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules (2013)
  7. Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew: AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems (2013)
  8. Zhang, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai: A Fourier-series-based kernel-independent fast multipole method (2011)
  9. Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew: AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems (2010)