high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Enhanced molecular dynamics performance with a programmable graphics processor

D. C. Rapaport

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Tags: Chemistry, Computational chemistry, Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia Quadro FX 770 M, Physics

November 13, 2010 by hgpu

Langevin dynamics simulations of biomolecules on graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

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Tags: Biological Physics, Biomolecules, Condensed matter, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 295, Physics, Soft Condensed Matter

November 12, 2010 by hgpu

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

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Tags: Bioinformatics, Biomolecular assemblies, Chemistry, CUDA, Dynamic force spectroscopy, Langevin dynamics, Molecular dynamics, nVidia, nVidia GeForce GTX 295

November 9, 2010 by hgpu

General purpose Molecular Dynamics Simulations on GPUs: Issues of Pair Forces and Scaling to large Clusters

Christian Trott, Lars Winterfeld

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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

November 9, 2010 by hgpu

A molecular docking system using CUDA

Youngtae Roh, Jun Lee, Sungjun Park, Jee I. Kim

Tags: Bioinformatics, Biology, Biophysics, Chemistry, Molecular dynamics

November 9, 2010 by hgpu

N-Body Simulations on GPUs

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

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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

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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

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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

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

See all packages

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high performance computing on graphics processing units: hgpu.org

Enhanced molecular dynamics performance with a programmable graphics processor

Langevin dynamics simulations of biomolecules on graphics processors

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

General purpose Molecular Dynamics Simulations on GPUs: Issues of Pair Forces and Scaling to large Clusters

A molecular docking system using CUDA

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)

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

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