Poisson Boltzmann

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Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

Ruxi Qi, Wesley M. Botello-Smith, Ray Luo

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Tags: Biomolecules, Biophysics, Boltzmann equation, Computational Physics, CUBLAS, CUDA, Electrostatics, Molecular simulation, nVidia, nVidia GeForce GTX 980 Ti, Physics, Poisson Boltzmann

April 11, 2017 by hgpu

A GPU-based Large-scale Monte Carlo Simulation Method for Systems with Long-range Interactions

Yihao Liang, Xiangjun Xing, Yaohang Li

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Tags: Algorithms, Computational Physics, CUDA, Monte Carlo simulation, nVidia, Physics, Poisson Boltzmann, Tesla K20

February 19, 2016 by hgpu

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

Christopher D. Cooper, Lorena A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

June 14, 2015 by hgpu

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

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Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

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

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

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, Intel Phi, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

September 17, 2013 by hgpu

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

Christopher Cooper, Lorena A. Barba

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Tags: Bioinformatics, Biophysics, Boltzmann equation, Computational Physics, Computer science, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

January 31, 2013 by hgpu

A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver

Weihua Geng, Ferosh Jacob

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Tags: Biomolecules, CUDA, Electrostatics, Linear Algebra, Mathematics, Molecular surface, Numerical Analysis, nVidia, Poisson Boltzmann, Tesla M2070

January 25, 2013 by hgpu

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger

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Tags: Biomolecules, Biophysics, Chemistry, Molecular simulation, nVidia, nVidia GeForce GTX 280, Poisson Boltzmann

January 25, 2011 by hgpu

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger

Tags: ASIC, Chemistry, Computational chemistry, MDGRAPE, Poisson Boltzmann, Solvent effects

October 29, 2010 by hgpu

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high performance computing on graphics processing units: hgpu.org

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

A GPU-based Large-scale Monte Carlo Simulation Method for Systems with Long-range Interactions

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

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

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Recent source codes

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LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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