high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

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Tags: Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenMP, Package

June 16, 2011 by hgpu

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Steffen Frey, Thomas Schlomer, Sebastian Grottel, Carsten Dachsbacher, Oliver Deussen, Thomas Ertl

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Tags: Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization, Voronoi diagram

June 15, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 2011 by hgpu

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Karl A. Wilkinson, Paul Sherwood, Martyn F. Guest, Kevin J. Naidoo

Tags: Chemistry, Fortran, Molecular dynamics, Molecular modeling, nVidia

May 21, 2011 by hgpu

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel

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Tags: Chemistry, CUDA, Floating point error, Molecular dynamics, nVidia, Tesla S1070

April 25, 2011 by hgpu

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

Gilad Shainer, Ali Ayoub, Pak Lui, Tong Liu, Michael Kagan, Christian Trott, Greg Scantlen, Paul Crozier

Tags: Computer science, Memory model, Molecular dynamics, Network communications, Networks, nVidia, Tesla

April 15, 2011 by hgpu

GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu

Tags: ATI, Brook, Chemistry, Molecular dynamics

April 5, 2011 by hgpu

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Canqun Yang, Qiang Wu, Juan Chen, Zhen Ge

Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Tesla C870

March 25, 2011 by hgpu

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

N. R. Hayre, R. R. Singh, D. L. Cox

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Tags: Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285

March 22, 2011 by hgpu

Fast heterogeneous computing with CUDA compatible Tesla GPU computing processor (personal supercomputing)

D. Kumar, M. A. Qadeer

Tags: Computer science, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, Tesla

March 8, 2011 by hgpu

General-purpose molecular dynamics simulations on GPU-based clusters

Christian R. Trott, Lars Winterfeld, Paul S. Crozier

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Source codes

Tags: Computational Physics, Condensed matter, CUDA, GPU cluster, Materials Science, Molecular dynamics, MPI, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Performance, Physics, Tesla C1060, Tesla S1070

March 8, 2011 by hgpu

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

A.P. Iliopoulos, J.G. Michopoulos, S.G. Lambrakos, N. Bernstein

Tags: Chemistry, Molecular dynamics, Performance

March 1, 2011 by hgpu

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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high performance computing on graphics processing units: hgpu.org

Brownian dynamics simulations on CPU and GPU with BD_BOX

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

GPGPU supported cooperative acceleration in molecular dynamics

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

Fast heterogeneous computing with CUDA compatible Tesla GPU computing processor (personal supercomputing)

General-purpose molecular dynamics simulations on GPU-based clusters

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

Recent source codes

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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