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Abstract: Short--range molecular dynamics simulations of molecular systems are commonly parallelized by replicated--data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2--, 3--, and 4--body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter--processor communication scales as N , the number of atoms, independent of P , the number of processors. Thus, their... (Update)
Context of citations to this paper: More
.... in practice they may lead to reasonable speedups on medium size computers (up to 128 processors) Spatial decomposition schemes (used in [11, 13]) where atoms are distributed into cubes depending on the spatial locations, and migrated among the cubes as needed, are shown to be...
...time steps, requiring extensive parallelization of computation within each timestep. For example, simulating a biomolecular system with 3762 atoms sequentially required only about 1 second for a single time step in a particular simulation. To run this computation e#ectively on...
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BibTeX entry: (Update)
Plimpton S. and Hendrickson B. A new parallel method for molecular dynamics simulation of macromolecular systems. Sandia Thechnical Report, SAN94-1862, 1994. http://citeseer.ist.psu.edu/plimpton94new.html More
@misc{ plimpton94new,
author = "S. Plimpton and B. Hendrickson",
title = "A new parallel method for molecular dynamics simulation of macromolecular
systems",
text = "Plimpton S. and Hendrickson B. A new parallel method for molecular dynamics
simulation of macromolecular systems. Sandia Thechnical Report, SAN94-1862,
1994.",
year = "1994",
url = "citeseer.ist.psu.edu/plimpton94new.html" }
Citations (may not include all citations):306 Computer Simulation of Liquids (context) - Allen, Tildesley - 1987
277 A fast algorithm for particle simulations - Greengard, Rokhlin - 1987 ACM
257 force--calculation algorithm (context) - Barnes, Hut et al. - 1986
120 CHARMM: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
57 Fast parallel algorithms for short--range molecular dynamics - Plimpton - 1995
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38 Numerical integration of the Cartesian equations of motion o.. (context) - Ryckaert, Ciccotti et al. - 1977
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27 Distributed memory matrix--vector multiplication and conjuga.. (context) - Lewis, Geijn - 1993
24 Building a high--performance collective communication librar.. - Barnett, Shuler et al. - 1994
23 Parallel molecular dynamics (context) - Clark, McCammon et al. - 1992 ACM DBLP
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11 Parallel LU decomposition on a transputer network (context) - Bisseling, Vorst - 1989 ACM DBLP
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9 A domain decomposition parallel processing algorithm for mol.. - Brown, Clarke et al. - 1994
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7 Parallelization of AMBER's molecular dynamics module for dis.. (context) - DeBolt, Kollman - 1993
6 Parallel molecular dynamics of biomolecules (context) - Schreiber, Steinhauser et al. - 1992 DBLP
6 Parallel many--body simulations without all--to--all communi.. - Hendrickson, Plimpton - 1995
5 A new decomposition strategy for parallel bonded molecular d.. (context) - Plimpton, Hendrickson et al. - 1993 DBLP
4 RATTLE: A velocity version of the SHAKE algorithm for molecu.. (context) - Andersen - 1983
4 Dynamic load balancing algorithms for replicated data molecu.. (context) - Young, Brooks
4 Parallelization of AMBER molecular dynamics program for the .. (context) - Sato, Tanaka et al. - 1992
3 Parallel macromolecular simulations and the replicated data .. (context) - Smith, Forester - 1994
2 Molecular dynamics simulation of a cyclic siloxane based liq.. (context) - Patnaik, Pachter et al. - 1993
2 Protein calculations on parallel processors: II (context) - Janak, Pattnaik - 1992
2 Parallel molecular dynamics with the embedded atom method - Plimpton, Hendrickson - 1992
1 Simulation of organic liquids using pseudo--pairwise interat.. (context) - Chynoweth, Klomp et al. - 1991
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