Point-centered domain decomposition for parallel molecular dynamics simulation

DOI10.1016/S0010-4655(99)00436-1zbMath0962.65006OpenAlexW2069737637MaRDI QIDQ1971523

R. Koradi, M. Billeter, Peter Güntert

Publication date: 15 February 2001

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

Full work available at URL: https://doi.org/10.1016/s0010-4655(99)00436-1

zbMATH Keywords

performanceMPIalgorithmparallel computingmolecular dynamicsmessage passingbiological macromoleculescluster atomsOPALpprotein cyclophilinVoronoi-like domain decomposition

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Parallel numerical computation (65Y05) Complexity and performance of numerical algorithms (65Y20) Stochastic particle methods (65C35)

Related Items (6)

A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape ⋮ Parallelization strategies for Monte Carlo simulations of thin film deposition ⋮ Parallel SPH modeling using dynamic domain decomposition and load balancing displacement of Voronoi subdomains ⋮ Dynamic domain decomposition method based on weighted Voronoi diagrams ⋮ A new parallel algorithm for constructing Voronoi tessellations from distributed input data ⋮ A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites

Uses Software

• MPI

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