A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers

DOI10.1016/J.CPC.2013.10.028zbMath1360.78047arXiv1309.4018OpenAlexW2056787579WikidataQ28655258 ScholiaQ28655258MaRDI QIDQ525761

Jaydeep P. Bardhan, Christopher D. Cooper, Lorena A. Barba

Publication date: 5 May 2017

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

Full work available at URL: https://arxiv.org/abs/1309.4018

zbMATH Keywords

boundary element methodPoisson-BoltzmannCUDAPythontreecodebiomolecular electrostaticsimplicit solvent

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Electro- and magnetostatics (78A30)

Related Items (4)

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code ⋮ GPU acceleration of the boundary element method for shear-deformable bending of plates ⋮ DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture ⋮ Iterative coupling algorithms for large multidomain problems with the boundary element method

Uses Software

• Unnamed Item
• CUDA
• APBS
• PyCUDA
• PDB2PQR
• PyOpenCL
• PyGBe
• TABI

Cites Work

• Unnamed Item
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A Cartesian treecode for screened Coulomb interactions
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics

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