Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns

DOI10.1016/j.cpc.2011.02.013zbMath1259.78044arXiv1007.4591OpenAlexW2067178485WikidataQ108784889 ScholiaQ108784889MaRDI QIDQ1943150

Tsuyoshi Hamada, Matthew G. Knepley, Jaydeep P. Bardhan, Rio Yokota, Lorena A. Barba

Publication date: 15 March 2013

Published in: Computer Physics Communications (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1007.4591

zbMATH Keywords

boundary element methodintegral equationsfast multipole methodGPUgraphics processorsbioelectrostatics

Mathematics Subject Classification ID

Statistical mechanics of polymers (82D60) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Software, source code, etc. for problems pertaining to optics and electromagnetic theory (78-04) Multipole methods applied to problems in optics and electromagnetic theory (78M16)

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Uses Software

• NAMD
• CUDA
• APBS
• CHARMM
• PetFMM
• SDA
• FFTSVD
• Fastcap
• VMD

Cites Work

• Condition number of the BEM matrix arising from the Stokes equations in 2D
• A kernel-independent adaptive fast multipole algorithm in two and three dimensions
• Quality mesh generation for molecular skin surfaces using restricted union of balls
• Rapid solution of integral equations of classical potential theory
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Calculation of isotropic turbulence using a pure Lagrangian vortex method
• Quality meshing of implicit solvation models of biomolecular structures
• PetFMM-A dynamically load-balancing parallel fast multipole library
• GPU-accelerated boundary element method for Helmholtz' equation in three dimensions
• GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems
• The Numerical Solution of Fredholm integral Equations of the Second Kind
• A fast algorithm for particle simulations