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

DOI10.1016/J.CPC.2010.12.021MaRDI QIDQ634064zbMATH OpenOpenAlexFDO

Authors W. Michael Brown, Peng Wang, Steven J. Plimpton, 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

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

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Numerical algorithms for specific classes of architectures (65Y10)

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Cites work

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

Cited in

(13)

• On the equivalence of the two foundational formulations for atomistic flux in inhomogeneous transport processes
• Arrested coarsening and large density fluctuations in driven particle mixtures in two dimensions
• High performance computing in multiscale problems of gas dynamics
• 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
• Fast multipole method for 3-D Poisson-Boltzmann equation in layered electrolyte-dielectric media
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
• 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
• LAMMPS -- a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
• Effect of initial temperature and pressure on thermal behavior of ethanol/oxygen fuel mixture with shock wave by molecular dynamics simulation
• A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions

Describes a project that uses

Uses Software

• Gromacs

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