AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems

doi:https://doi.org/10.1016/j.cpc.2010.02.015

Title: AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems

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Abstract

A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.

Authors:

Lu, Benzhuo ^[1]; Cheng, Xiaolin ^[1]; Huang, Jingfang ^[1]; McCammon, Jonathan ^[1]

ORNL

Publication Date:: 2010-01-01

Research Org.:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 981807

DOE Contract Number:: DE-AC05-00OR22725

Resource Type:: Journal Article

Journal Name:: Computer Physics Communications

Additional Journal Information:: Journal Volume: 181; Journal Issue: 6; Journal ID: ISSN 0010-4655

Country of Publication:: United States

Language:: English

Subject:: 97 MATHEMATICAL METHODS AND COMPUTING; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ALGORITHMS; A CODES; ELECTROSTATICS; INTEGRAL EQUATIONS; MULTIPOLES; BIOLOGICAL MATERIALS; NUMERICAL SOLUTION

Citation Formats


                    Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems.  United States: N. p., 2010. 
        Web.  doi:10.1016/j.cpc.2010.02.015.

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                    Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, & McCammon, Jonathan. AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems.  United States.  https://doi.org/10.1016/j.cpc.2010.02.015

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                    Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. Fri .  
        "AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems".  United States.  https://doi.org/10.1016/j.cpc.2010.02.015.

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@article{osti_981807,

  title        = {AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems},

  author       = {Lu, Benzhuo and Cheng, Xiaolin and Huang, Jingfang and McCammon, Jonathan},

  abstractNote = {A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.},

  doi          = {10.1016/j.cpc.2010.02.015},

  url          = {https://www.osti.gov/biblio/981807},
  journal      = {Computer Physics Communications},

  issn         = {0010-4655},

  number       = 6,

  volume       = 181,

  place        = {United States},

  year         = {2010},

  month        = {1}

}

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Journal Article:

https://doi.org/10.1016/j.cpc.2010.02.015

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