Implementing molecular dynamics on hybrid high performance computers-short range forces

DOI10.1016/j.cpc.2010.12.021zbMath1221.82008OpenAlexW2168363974MaRDI QIDQ634064

Steven J. Plimpton, W. Michael Brown, Peng Wang, Arnold N. Tharrington

Publication date: 2 August 2011

Published in: Computer Physics Communications (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.cpc.2010.12.021

zbMATH Keywords

molecular dynamicsGPU\texttt{CUDA}\texttt{OpenCL}hybrid parallel computingmolecular dynamics package \texttt{LAMMPS}

Mathematics Subject Classification ID

Related Items (11)

Fast multipole method for 3-D Poisson-Boltzmann equation in layered electrolyte-dielectric media ⋮ Massively parallel Monte Carlo for many-particle simulations on GPUs ⋮ A fast mollified impulse method for biomolecular atomistic simulations ⋮ A cross-platform, high-performance SPH toolkit for image-based flow simulations on the pore scale of porous media ⋮ A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions ⋮ GPU-based molecular dynamics of turbulent liquid flows with OpenMM ⋮ Develop a molecular dynamics approach to simulate the single-/multi-layer CsGeX\(_3\) (X = I, Cl, and Br) perovskite stress-strain structure at different temperatures and pressures for solar cell in building energy management ⋮ LAMMPS -- a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales ⋮ High performance computing in multiscale problems of gas dynamics ⋮ Efficient implementation of the many-body reactive bond order (REBO) potential on GPU ⋮ On the equivalence of the two foundational formulations for atomistic flux in inhomogeneous transport processes

Uses Software

• Gromacs

Cites Work

• Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics
• GPU accelerated molecular dynamics simulation of thermal conductivities
• General purpose molecular dynamics simulations fully implemented on graphics processing units
• A new version of the fast multipole method for screened Coulomb interactions in three dimensions
• Bioinformatics and computational biology. First international conference, BICoB 2009, New Orleans, LA, USA, April 8--10, 2009. Proceedings
• Fast parallel algorithms for short-range molecular dynamics
• Cohesion

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