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Fast binding site mapping using GPUs and CUDA

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060

January 11, 2011 by hgpu

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Muller-Wittig

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX

January 10, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter

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Tags: Biology, Cell processor, Cg, Computational biology, Molecular dynamics, nVidia, nVidia GeForce 7900 GTX

January 2, 2011 by hgpu

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Nathan Schmid, Mathias Botschi, Wilfred F. Van Gunsteren

Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, nVidia Quadro FX 5800, Solvent effects

December 17, 2010 by hgpu

Molecular Dynamics on a Grand Scale

Matthew James Mawson Breeze

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Tags: ATI, ATI Radeon X1600, Chemistry, GLSL, Molecular dynamics, nVidia, nVidia GeForce 6200, nVidia GeForce 8800 GTS, OpenGL, Thesis

December 17, 2010 by hgpu

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

W. Liu, B. Schmidt, G. Voss, W. Mullerwittig

Tags: Chemistry, CUDA, Molecular dynamics, nVidia

December 11, 2010 by hgpu

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Ian Tunbridge, Robert B. Best, James Gain, Michelle M. Kuttel

Tags: Chemistry, Molecular dynamics

December 7, 2010 by hgpu

Fast multipole methods on a cluster of GPUs for the meshless simulation of turbulence

R. Yokota, T. Narumi, R. Sakamaki, S. Kameoka, S. Obi, K. Yasuoka

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Tags: CUDA, Fast multipole method, Fluid dynamics, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce 8800 GT, Physics

November 28, 2010 by hgpu

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Feiguo Chen, Wei Ge, Jinghai Li

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Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, MPI, nVidia, Tesla C870

November 27, 2010 by hgpu

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, Molecular modeling, nVidia, nVidia GeForce GTX 295

November 25, 2010 by hgpu

GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten

Tags: Chemistry, Molecular dynamics, Molecular modeling

November 22, 2010 by hgpu

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

See all packages

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high performance computing on graphics processing units: hgpu.org

Fast binding site mapping using GPUs and CUDA

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Molecular Dynamics on a Grand Scale

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Fast multipole methods on a cluster of GPUs for the meshless simulation of turbulence

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

GPU-accelerated molecular modeling coming of age

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

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