Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver
نویسندگان
چکیده
منابع مشابه
Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver
This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fas...
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1 State Key Laboratory of Scientific/Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China. 2 Oak Ridge National Lab and the University of Tennesse. 3 Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599-3250. 4 Department of Chem...
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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...
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We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed memory computers. As a result, the new version can easily handle larger molecules or situations with higher accuracy requirements. To demonstrate the updated...
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ژورنال
عنوان ژورنال: Communications in Computational Physics
سال: 2013
ISSN: 1815-2406,1991-7120
DOI: 10.4208/cicp.210711.111111s