high performance computing on graphics processing units: hgpu.org

hgpu.org » Electrostatic potential

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Marcos Novalbos, Jaime Gonzalez, Miguel A. Otaduy, Roberto Martinez Benito, Alberto Sanchez

View

Tags: Algorithms, Biomolecules, Chemistry, CUDA, Electrostatic potential, Electrostatics, FFT, Molecular dynamics, Multilevel summation, N-body simulation, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX Titan

September 15, 2014 by hgpu

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

View

Download (PDF)

Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

Raul Ernesto Torres Carvajal

View

Download (PDF)

Tags: Algorithms, Chemistry, Cluster analysis, CUDA, Electrostatic potential, Electrostatics, nVidia, nVidia GeForce GT 240, Pattern recognition, Thesis

December 29, 2011 by hgpu

Development of an unified FDTD-FEM library for electromagnetic analysis with CPU and GPU computing

Jorge Frances Monllor, Sergio Bleda Perez, Sergi Gallego Rico, Cristian Neipp Lopez, Andres Marquez Ruiz, Inmaculada Pascual Villalobos, Augusto Belendez Vazquez

View

Download (PDF)

Tags: CUDA, Electrodynamics, Electrostatic potential, Electrostatics, FDTD, FEM, Finite element method, Finite-difference time-domain, nVidia, nVidia GeForce GTX 470

December 13, 2011 by hgpu

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer

Tags: Algorithms, Chemistry, Computational chemistry, Electrostatic potential, Electrostatics, Molecular dynamics

August 8, 2011 by hgpu

Towards accelerating molecular modeling via multi-scale approximation on a GPU

M. Daga, Wu-chun Feng, T. Scogland

Tags: Algorithms, Biomolecules, Electrostatic potential, Medicine, Molecular modeling

May 5, 2011 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

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

Development of an unified FDTD-FEM library for electromagnetic analysis with CPU and GPU computing

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Towards accelerating molecular modeling via multi-scale approximation on a GPU

Accelerating molecular modeling applications with graphics processors

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Most viewed papers (last 30 days)