high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

N-Body Simulations on GPUs

Erich Elsen, V. Vishal, Mike Houston, Vijay Pande, Pat Hanrahan, Eric Darve

View

Tags: ATI, ATI Radeon X1900, ATI Stream, Brook, Computational Engineering, Computer science, Molecular dynamics, N-body simulation, Stellar dynamics

November 8, 2010 by hgpu

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

Alfeus Sunarso, Tomohiro Tsuji, Shigeomi Chono

Tags: Computational Physics, Liquid crystals, Molecular dynamics, Physics

November 7, 2010 by hgpu

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

P. Eastman, V. S. Pande

Tags: Chemistry, Computational chemistry, Molecular dynamics, Solvent effects

November 7, 2010 by hgpu

MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre

View

Download (PDF)

Source codes

Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Package, Python

November 6, 2010 by hgpu

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, G. De Fabritiis

Tags: Biochemistry, Chemistry, Molecular dynamics, Thermodynamics

November 6, 2010 by hgpu

Iterative induced dipoles computation for molecular mechanics on GPUs

Frederico Pratas,Ricardo A. Mata,Leonel Sousa

View

Download (PDF)

Tags: Chemistry, Computational chemistry, Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GT, nVidia GeForce GTX 285

November 5, 2010 by hgpu

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp, Vijay S. Pande

Tags: Bioinformatics, Biology, Chemistry, Molecular dynamics

November 4, 2010 by hgpu

Harvesting graphics power for MD simulations

J. A. van Meel, A. Arnold, D. Frenkel, Portegies S. F. Zwart, R. G. Belleman

View

Download (PDF)

Tags: Condensed matter, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, Soft Condensed Matter

November 3, 2010 by hgpu

Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Ji Xu, Ying Ren, Wei Ge, Xiang Yu, Xiaozhen Yang, Jinghai Li

View

Download (PDF)

Tags: CUDA, Macromolecule, Materials Science, Molecular dynamics, nVidia, nVidia GeForce GT 200, Soft Condensed Matter

November 3, 2010 by hgpu

Multilevel summation of electrostatic potentials using graphics processing units

David J. Hardy, John E. Stone, Klaus Schulten

View

Download (PDF)

Tags: Chemistry, CUDA, Electrostatics, Molecular dynamics, Molecular modeling, Multilevel summation, nVidia, nVidia GeForce GTX 280, Physics, Tesla C870, Tesla D870

November 2, 2010 by hgpu

Fast and accurate protein substructure searching with simulated annealing and GPUs

Alex D. Stivala, Peter J. Stuckey, Anthony I. Wirth

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biological Physics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285, Package, Tesla C1060

November 2, 2010 by hgpu

General purpose molecular dynamics simulations fully implemented on graphics processing units

J. Anderson, C. Lorenz, A. Travesset

View

Download (PDF)

Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, Physics, Polymer Systems

November 2, 2010 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

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

N-Body Simulations on GPUs

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

MDLab: A molecular dynamics simulation prototyping environment

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

Iterative induced dipoles computation for molecular mechanics on GPUs

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Harvesting graphics power for MD simulations

Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Multilevel summation of electrostatic potentials using graphics processing units

Fast and accurate protein substructure searching with simulated annealing and GPUs

General purpose molecular dynamics simulations fully implemented on graphics processing units

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

Most viewed papers (last 30 days)