AFMPB swMATH ID: 8875 Software Authors: Lu, B.; Cheng, X.; Huang, J.; Mccammon, J. A. Description: 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. Homepage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880819/ Keywords: Poisson-Boltzmann equation; boundary integral equation; node-patch method; Krylov subspace methods; fast multipole methods; diagonal translations; software tool { t AFMPB} Related Software: MIBPB; APBS; TMSmesh; tabipb; PAFMPB; TABI; SDPBS; DelPhi; Apbsmem; FFTSVD; UHBD; DelPhi Web Server; SyFi; FEniCS; VCMM; SMPBS; SG; CHARMM; Gromacs; NAMD Cited in: 14 Documents all top 5 Cited by 33 Authors 7 Lu, Benzhuo 4 Huang, Jingfang 3 Ying, Jinyong 3 Zhang, Bo 2 Cheng, Xiaolin 2 Li, Jiao 2 McCammon, J. Andrew 2 Pitsianis, Nikos P. 2 Sun, Xiaobai 1 Alexov, Emil 1 Chen, Minhong 1 Debuhr, Jackson 1 Dou, Wei 1 Fan, Ronghong 1 Geng, Weihua 1 Gui, Sheng 1 Krasny, Robert 1 Li, Chuan 1 Li, Hongliang 1 Li, Lin 1 Maday, Yvon 1 Mayolo, Silvio 1 Niedzielski, Drake 1 Peng, Bo 1 Petukh, Marharyta 1 Quan, Chaoyu 1 Stamm, Benjamin 1 Sterling, Thomas Lawrence 1 Wu, Hao 1 Xie, Dexuan 1 Zhang, Qianru 1 Zhou, Shenggao 1 Zou, Qingsong all top 5 Cited in 6 Serials 5 Journal of Computational Physics 4 Computer Physics Communications 2 International Journal of Numerical Analysis and Modeling 1 SIAM Journal on Scientific Computing 1 Communications in Computational Physics 1 Molecular Based Mathematical Biology all top 5 Cited in 8 Fields 11 Numerical analysis (65-XX) 7 Optics, electromagnetic theory (78-XX) 6 Biology and other natural sciences (92-XX) 3 Partial differential equations (35-XX) 2 Computer science (68-XX) 1 Harmonic analysis on Euclidean spaces (42-XX) 1 Fluid mechanics (76-XX) 1 Statistical mechanics, structure of matter (82-XX) Citations by Year