A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver

DOI10.1016/J.CPC.2013.01.017MaRDI QIDQ463018zbMATH OpenOpenAlexFDO

Authors Weihua Geng, Ferosh Jacob

Publication date 23 October 2014

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

Full work available at URL https://arxiv.org/abs/1301.5885

zbMATH Keywords

parallel computingelectrostaticsboundary integralPoisson-Boltzmanngraphic processing units (GPU)

Mathematics Subject Classification ID

Electro- and magnetostatics (78A30) 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)

Abstract: In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only $11N+6N_c$ size-of-double device memory for a biomolecule with $N$ triangular surface elements and $N_c$ partial charges. Numerical tests of these schemes show well-maintained accuracy and fast convergence. The GPU implementation using one GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation using one CPU (Intel L5640 2.27GHz). With our approach, solving PB equations on well-discretized molecular surfaces with up to 300,000 boundary elements will take less than about 10 minutes, hence our approach is particularly suitable for fast electrostatics computations on small to medium biomolecules.

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Cites work

• scientific article; zbMATH DE number 5038548 (Why is no real title available?)
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems
• Multiscale molecular dynamics using the matched interface and boundary method
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems

Cited in

(18)

• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
• A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
• Fast evaluation of Helmholtz potential on graphics processing units (GPUs)
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
• A GPU-accelerated fast multipole method based on barycentric Lagrange interpolation and dual tree traversal
• Optimized parallelization of boundary integral Poisson-Boltzmann solvers
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Multi-core CPU or GPU-accelerated multiscale modeling for biomolecular complexes
• Graphical processing unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels
• A versatile algorithm for the treatment of open boundary conditions in smoothed particle hydrodynamics GPU models
• Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces

Describes a project that uses

Uses Software

• tabipb
• TABI
• TMSmesh
• MIBPB
• APBS
• CUDA
• NAMD
• AMBER

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