high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Accelerating Density Functional Calculations with Graphics Processing Unit

Koji Yasuda

Tags: Chemistry, Computational chemistry, Molecular modeling

October 30, 2010 by hgpu

Accelerating molecular modeling applications with graphics processors

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten

View

Download (PDF)

Tags: Chemistry, Computational chemistry, CUDA, Electrostatic potential, Molecular dynamics, Molecular modeling, Multilevel summation, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

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

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger

Tags: ASIC, Chemistry, Computational chemistry, MDGRAPE, Poisson Boltzmann, 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

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

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

* * *

Clava: C/C++ Source-to-Source Tool based on Clang

Challenges and Opportunities in C/C++ Source-To-Source Compilation

gpuLik

Statistical Computing With Graphics Processing Units

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Applications

Accelerating Density Functional Calculations with Graphics Processing Unit

Accelerating molecular modeling applications with graphics processors

Accelerating molecular dynamic simulation on graphics processing units

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

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

GPU acceleration of cutoff pair potentials for molecular modeling applications

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

GPU acceleration of a production molecular docking code

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Recent source codes

Clava: C/C++ Source-to-Source Tool based on Clang

gpuLik

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

DeepAxe: A Framework for Exploration of Approximation and Reliability Trade-offs in DNN Accelerators

RTIndeX: Exploiting Hardware-Accelerated GPU Raytracing for Database Indexing

Most viewed papers (last 30 days)