high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

View

Download (PDF)

Source codes

Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

David Dynerman, Erick Butzlaff, Julie C. Mitchell

View

Download (PDF)

Tags: Bioinformatics, Biology, Biophysics, Chemistry, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Solvent effects

October 29, 2010 by hgpu

GPU acceleration of cutoff pair potentials for molecular modeling applications

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen Mei

View

Download (PDF)

Tags: Algorithms, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, Tesla C870

October 28, 2010 by hgpu

Adapting a message-driven parallel application to GPU-accelerated clusters

James C. Phillips, John E. Stone, Klaus Schulten

View

Download (PDF)

Tags: Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia Quadro FX 5600

October 28, 2010 by hgpu

GPU-accelerated large-scale quantum molecular dynamics simulation of 3-dimensional C60 polymers

Toshiaki Iitaka

View

Download (PDF)

Tags: Computational Physics, CUDA, Materials Science, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, Physics

October 28, 2010 by hgpu

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

M. J. Harvey, G. De Fabritiis

Tags: Chemistry, Computational chemistry, Molecular dynamics, nVidia

October 28, 2010 by hgpu

GPU acceleration of a production molecular docking code

Bharat Sukhwani, Martin C. Herbordt

View

Download (PDF)

Tags: Bioinformatics, Biophysics, Chemistry, FPGA, Molecular dynamics, nVidia, Tesla C1060

October 27, 2010 by hgpu

GPU accelerated molecular dynamics simulation of thermal conductivities

Juekuan Yang, Yujuan Wang, Yunfei Chen

Tags: Computational Physics, Molecular dynamics, nVidia, Physics

October 27, 2010 by hgpu

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

M. J. Harvey, G. Giupponi, G. De Fabritiis

View

Download (PDF)

Tags: Biological Physics, Chemistry, Computational Physics, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Physics, Tesla C1060

October 27, 2010 by hgpu

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

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Accelerating molecular dynamic simulation on graphics processing units

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

GPU acceleration of cutoff pair potentials for molecular modeling applications

Adapting a message-driven parallel application to GPU-accelerated clusters

GPU-accelerated large-scale quantum molecular dynamics simulation of 3-dimensional C60 polymers

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

GPU acceleration of a production molecular docking code

GPU accelerated molecular dynamics simulation of thermal conductivities

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Recent source codes

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

XaaS containers

CASS: Cuda-Amd aSSembly

Cluser of smartphones for edge computing application using TensorFlow

SYCL Container

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

Most viewed papers (last 30 days)