high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Yaohang Li, Douglas Wardell, Vincent Freeh

View

Download (PDF)

Tags: Algorithms, Biology, Molecular dynamics

February 24, 2011 by hgpu

Production Floating Point Applications on FPGAs

Martin C. Herbordt, Bharat Sukhwani, Matt Chiu, Md. Ashfaq Khan

View

Download (PDF)

Tags: Chemistry, Computer science, CUDA, FPGA, Molecular dynamics, Molecular modeling, nVidia, Tesla C1060

February 22, 2011 by hgpu

Simulations of Large Membrane Regions using GPU-enabled Computations – Preliminary Results

Narayan Ganesan, Michela Taufer, Sandeep Patel

View

Download (PDF)

Tags: Chemistry, CUDA, Membrane computing, Molecular dynamics, nVidia, Performance

February 17, 2011 by hgpu

High-precision molecular dynamics simulation of UO2-PuO2: superionic transition in uranium dioxide

S.I. Potashnikov, A.S. Boyarchenkov, K.A. Nekrasov, A.Ya. Kupryazhkin

View

Download (PDF)

Tags: Condensed matter, CUDA, Materials Science, Molecular dynamics, nVidia, Physics

February 9, 2011 by hgpu

High-precision molecular dynamics simulation of UO2-PuO2: pair potentials comparison

S.I. Potashnikov, A.S. Boyarchenkov, K.A. Nekrasov, A.Ya. Kupryazhkin

View

Download (PDF)

Tags: Condensed matter, CUDA, Materials Science, Molecular dynamics, nVidia, Physics

February 9, 2011 by hgpu

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units – Radial Distribution Function Histogramming

Benjamin G. Levine, John E. Stone, Axel Kohlmeyer

View

Download (PDF)

Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 480, Tesla C1060, Tesla C2050, Tesla S1070

February 9, 2011 by hgpu

Two Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, Ivan Viola, Nathalie Reuter, Helwig Hauser

View

Download (PDF)

Tags: Biology, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, OpenGL, Visualization

February 4, 2011 by hgpu

Molecular dynamics simulation of the supercooled Al melt on GPUs

Roman Bystryi, Andrey Kazennov, Igor Morozov, Vasily Pisarev, Vladimir Stegailov

View

Download (PDF)

Tags: Molecular dynamics, nVidia, nVidia GeForce GTX 260, Physics

January 25, 2011 by hgpu

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

I. V. Morozov, A. M. Kazennov, R. G. Bystryi, G. E. Norman, V. V. Pisarev, V. V. Stegailov

Tags: Molecular dynamics, nVidia, nVidia GeForce GTX 260, Physics

January 25, 2011 by hgpu

Efficient Parallel Implementation of Molecular Dynamics with Embedded Atom Method on Multi-core Platforms

Changjun Hu, Yali Liu, Jianjiang Li

Tags: Chemistry, Molecular dynamics, Molecular simulation, OpenMP

January 25, 2011 by hgpu

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

Prateek K. Jha, Rastko Sknepnek, Guillermo I. Guerrero-Garcia, Monica Olvera de la Cruz

Tags: Chemistry, Molecular dynamics

January 25, 2011 by hgpu

Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

David S. Cerutti, David A. Case

Tags: Chemistry, Molecular dynamics, Molecular simulation

January 25, 2011 by hgpu

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations

microSYCL: SYCL micro-benchmarks repository

Exploring SYCL as a Portability Layer for High-Performance Computing on CPUs

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Production Floating Point Applications on FPGAs

Simulations of Large Membrane Regions using GPU-enabled Computations – Preliminary Results

High-precision molecular dynamics simulation of UO2-PuO2: superionic transition in uranium dioxide

High-precision molecular dynamics simulation of UO2-PuO2: pair potentials comparison

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units – Radial Distribution Function Histogramming

Two Level Approach to Efficient Visualization of Protein Dynamics

Molecular dynamics simulation of the supercooled Al melt on GPUs

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

Efficient Parallel Implementation of Molecular Dynamics with Embedded Atom Method on Multi-core Platforms

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

Recent source codes

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

Most viewed papers (last 30 days)