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Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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

February 28, 2011 by hgpu

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Yaohang Li, Douglas Wardell, Vincent Freeh

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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

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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

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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

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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

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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

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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

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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

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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

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

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high performance computing on graphics processing units: hgpu.org

Accelerating Molecular Dynamics Simulations with GPUs

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

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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