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AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
Lu, Benzhuo1; Cheng, Xiaolin2; Huang, Jingfang3; McCammon, J. Andrew4
AbstractA 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 //lsec cc ac cn/-lubz/afmpb html and a mirror site at http //mccammon ucsd edu/ This paper is a brief summary of the program the algorithms, the implementation and the usage Program summary Program title AFMPB Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier AEGB_v1_0 Program summary URL http / lcpc cs qub ac uk/sunlmaries/AEGBvI.0 html Program obtainable from CPC Program Library. Queen's University, Belfast. N Ireland Licensing provisions GPL 2 0 No of lines in distributed program, including test data, etc 453 649 No of bytes in distributed program, including test data, etc 8 764 754 Distribution format tar gz Programming language Fortran Computer Any Operating system Any RAM Depends on the size of the discretized biomolecular system Classification 3 External routines Pre- and post-processing tools are required for generating the boundary elements and for visualization Users can use MSMS (hap //www scripps edu/-sanner/html/msms_home html) for preprocessing. and VMD (http //www ks unic eclu/Research/vmd/) for visualization S ub-programs included An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad (hap //www-users cs umn edu/-saad/software/SPARSKIT/sparskit html), and the fast multipole methods subroutines from FMMSuite (http //www.fastmultipole org/) Nature of problem Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions Solution method A novel node-patch scheme is used to discretize the well-conditioned boundary integral equation formulation of the linearized Poisson-Boltzmann equation Various Krylov subspace solvers can be subsequently applied to solve the resulting linear system, with a bounded number of iterations independent of the number of discretized unknowns The matrix-vector multiplication at each iteration is accelerated by the adaptive new versions of fast multipole methods The AFMPB solver requires other stand-alone pre-processing tools for boundary mesh generation, post-processing tools for data analysis and visualization, and can be conveniently coupled with different time stepping methods for dynamics simulation Restrictions Only three or six significant digits options are provided in this version Unusual features Most of the codes are in Fortran77 style Memory allocation functions from Fortran90 and above are used in a few subroutines Additional comments The current version of the codes is designed and written for single core/processor desktop machines Check htip //lsec cc ac cn/-lubz/afmpb html and Imp //mccammon ucsd edu/ for updates and changes Running time The running time varies with the number of discretized elements (N) in the system and their distributions In most cases. it scales linearly as a function of N (C) 2010 Elsevier B V All rights reserved
KeywordPoisson-Boltzmann equation Boundary integral equation Node-patch method Krylov subspace methods Fast multipole methods Diagonal translations
Funding ProjectHHMI ; NIH ; NBCR ; NSF[NSF0811130] ; NSF[NSF0411920] ; NSF[MCB0506593] ; NSF Center of Theoretical Biological Physics (CTBP) ; Institute for Mathematics and Its Applications ; Academy of Mathematics and Systems Science of Chinese Academy of Sciences ; State Key Laboratory of Scientific/Engineering Computing ; NSFC[NSFC10971218] ; US. Department of Energy[ERKJE84]
WOS Research AreaComputer Science ; Physics
WOS SubjectComputer Science, Interdisciplinary Applications ; Physics, Mathematical
WOS IDWOS:000277954400019
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Document Type期刊论文
Corresponding AuthorLu, Benzhuo
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, Inst Computat Math & Sci Engn Comp, State Key Lab Sci Engn Comp, Beijing 100190, Peoples R China
2.Oak Ridge Natl Lab, Ctr Biophys Mol, Oak Ridge, TN 37831 USA
3.Univ N Carolina, Dept Math, Chapel Hill, NC 27599 USA
4.Univ Calif San Diego, Howard Hughes Med Inst, Dept Pharmacol, Dept Chem & Biochem,Ctr Theoret Biol Phys, La Jolla, CA 92093 USA
Recommended Citation
GB/T 7714
Lu, Benzhuo,Cheng, Xiaolin,Huang, Jingfang,et al. AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems[J]. COMPUTER PHYSICS COMMUNICATIONS,2010,181(6):1150-1160.
APA Lu, Benzhuo,Cheng, Xiaolin,Huang, Jingfang,&McCammon, J. Andrew.(2010).AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems.COMPUTER PHYSICS COMMUNICATIONS,181(6),1150-1160.
MLA Lu, Benzhuo,et al."AFMPB: An adaptive fast multipole, Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems".COMPUTER PHYSICS COMMUNICATIONS 181.6(2010):1150-1160.
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