Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

DOI10.1016/j.cpc.2014.12.022zbMath1344.78004OpenAlexW2115003574MaRDI QIDQ311614

Xiaobai Sun, Bo Zhang, Nikos P. Pitsianis, Benzhuo Lu, Bo Peng, Jingfang Huang

Publication date: 13 September 2016

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

Full work available at URL: https://doi.org/10.1016/j.cpc.2014.12.022

zbMATH Keywords

boundary integral equationparallelizationPoisson-Boltzmann equationautomatic surface meshingCilk Plusfast multipole methodssolvation free energy

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Parallel numerical computation (65Y05) 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)

Related Items (6)

Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces ⋮ A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models ⋮ Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation ⋮ Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations ⋮ DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture ⋮ PAFMPB

Uses Software

• APBS
• Cilk
• AFMPB
• TMSmesh
• TABI
• tabipb
• VCMM

Cites Work

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• Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A new version of the fast multipole method for screened Coulomb interactions in three dimensions
• NP-complete scheduling problems
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
• A fast algorithm for particle simulations

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