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

DOI10.1016/J.CPC.2013.01.017zbMATH Open1310.78017arXiv1301.5885OpenAlexW1994662101MaRDI QIDQ463018FDOQ463018

Authors: Weihua Geng, Ferosh Jacob 

Publication date: 23 October 2014

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

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.

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

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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)

Cites Work

• GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems
• Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• Multiscale molecular dynamics using the matched interface and boundary method
• Title not available (Why is that?)

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
• Fast evaluation of Helmholtz potential on graphics processing units (GPUs)
• A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• 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

Uses Software

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

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