David Brown, Hervé Minoux, Bernard Maigret  Home/Search
Context Related
| incm.unancy.fr/Chercheurs/Davi...DD.ps lctn.unancy.fr/Chercheurs/Davi...DD.ps Cached: PS.gz PS PDF This document uses CoBlitz to cache paper downloads. If your firewall is blocking outgoing connections to port 3125, you can use these links to download local copies.
Image Update HelpPS.gz PS PDF From: incm.unancy.fr/Chercheurs/...pub (more) (Enter author homepages) |
Rate this article:      (best)Comment on this article |
Abstract: We describe in this paper methods for applying domain decomposition to a general purpose molecular dynamics program. The algorithm is suitable for either distributed memory parallel computers or shared memory machines with message passing libraries. A method is discussed in detail which allows molecules of arbitrary connectivity to be simulated within the domain decomposition approach. The algorithm also contains techniques to handle both rigid bond constraints and special CH 2 constraints... (Update)
Context of citations to this paper: More
...decomposition uses linked lists and scales very well [80] but it is more difficult to implement and extend. It is used in ddgmq [16], SIGMA [53] NAMD2 [66] PMD [125] EulerGromos [22] DMMD [4] and evaluated in [9] SPRINGS (see paper [C] 4.1 Load balancing A good...
...d) Spatial decomposition, which uses linked lists and scales very well, but it is more difficult to write and extend. It is used in ddgmq [3], SIGMA, NAMD2 [8] PMD [19] EulerGromos [4] and it is evaluated in references [1, 9] 3.1 Work Distribution and Data Transfer Work...
Cited by: More
Overcoming instabilities in Verlet-I/r-RESPA with.. - Izaguirre, Ma.. (Correct)
Unknown - Protomol Molecular Dynamics (Correct)
A Tutorial on the Prototyping of Multiple Time.. - Izaguirre.. (2001) (Correct)
Active bibliography (related documents): More All
1.5: DL POLY: A Macromolecular Simulation Package - Smith Daresbury (Correct)
1.1: IMD: A Software Package For Molecular Dynamics Studies.. - Stadler, Mikulla, Trebin (1997) (Correct)
0.5: Algorithms for Constrained Molecular Dynamics - Eric Barth, Krzysztof.. (1995) (Correct)
Similar documents based on text: More All
0.2: Geometric Control for Atomic Systems - Schirmer (Correct)
0.1: Modelling The Active Site Of Glyceraldehyde-3.. - Cartier, Brown.. (Correct)
0.1: Optimization of Flexible Coupling in Domain Decomposition for .. - Van Der Maarel (Correct)
Related documents from co-citation: More All
9: Parallelizing molecular dynamics using spatial decomposition - Clark, Hanxleden et al. - 1994
9: Parallelization of charmm for mimd machines (context) - Brooks, Hodoscek - 1992
8: Parallelizing molecular dynamics programs for distributed memory machines - Hwang - 1995
BibTeX entry: (Update)
D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki. A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers. Comp. Phys. Comm., 83:1--13, 1994. http://citeseer.ist.psu.edu/brown97domain.html More
@article{ brown94domain,
author = "David Brown and Julian H. R. Clarke and Motoi Okuda and Takao Yamazaki",
title = "A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers",
journal = "Computer Physics Communications",
volume = "83",
pages = "1--13",
year = "1994",
url = "citeseer.ist.psu.edu/brown97domain.html" }
Citations (may not include all citations):306 Computer Simulation of Liquids (context) - Allen, Tildesley - 1987
20 Molecular Dynamics Simulation: Elementary Methods (context) - Haile - 1992
15 Understanding molecular simulation: from algorithms to appli.. (context) - Frenkel, Smit - 1996
5 York and L (context) - Darden - 1993
4 Ciccotti and H (context) - Ryckaert - 1977
4 Molecular Simulation (context) - Fincham - 1987
3 Journal Of Computational Physics (context) - Esselink, Hilbers - 1993
3 Journal Of Computational Physics (context) - Plimpton - 1995
2 Journal Of Chemical Physics (context) - York, Yang - 1994
2 Computer Physics Communications (context) - Smith - 1992
2 Molecular Physics (context) - Ryckaert - 1985
2 Computer Physics Communications (context) - Kutteh, Nicholas - 1995
2 Journal Of Chemical Physics (context) - Zhou, Berne - 1995
2 Parallel Computing (context) - Beazley, Lomdahl - 1994 ACM
2 Journal Of Chemical Physics (context) - York, Darden et al. - 1993
2 Computer Physics Communications (context) - Smith, Pettitt - 1995
2 Molecular Simulation (context) - Pinches, Tildesley et al. - 1991
2 Brown and J (context) - Liem - 1991
2 Brown and J (context) - Liem - 1992
2 Fincham and W (context) - Raine - 1989
2 Klomp and L (context) - Chynoweth - 1991
2 Computer Physics Communications (context) - Kutteh, Nicholas - 1995
1 Fujitsu Scientific & Technical Journal (context) - Sato, Tanaka et al. - 1992
1 Journal Of Computational Chemistry (context) - Janak, Pattnaik - 1992
1 Journal Of Computational Chemistry (context) - Shimada, Kaneko et al. - 1994
1 Journal Of Computational Chemistry (context) - Debolt, Kollman - 1993
1 Molecular Simulation (context) - Luty, Davis et al. - 1994
1 Journal Of Physical Chemistry (context) - Zhou, Schulten - 1995
1 Acs Symposium Series (context) - Mattson, Ravishanker - 1995
1 Journal Of Chemical Physics (context) - Essmann, Perera et al. - 1995
1 Computer Physics Communications (context) - Nakano, Kalia et al. - 1994
1 Ieee Computational Science & Engineering (context) - Hwang, Das et al. - 1995
1 Journal Of Physical Chemistry (context) - Luty, van Gunsteren - 1996
1 Chemical Physics Letters (context) - Board, Causey et al. - 1992
1 Journal Of Physical Chemistry (context) - Procacci, Darden et al. - 1996
1 Chemical Physics (context) - Schreiber, Steinhauser - 1992
1 Maraganore and Z (context) - Savage, Marzec et al. - 1990
1 Journal Of Chemical Physics (context) - Petersen - 1995
1 Journal Of Parallel and Distributed Computing (context) - Eisenhauer, Schwan - 1996
1 Molecular Simulation (context) - Hedman, Laaksonen - 1995
1 Computer Physics Communications (context) - Esselink - 1995
1 Gould and P (context) - Garsky, Lumma et al. - 1989
1 Journal Of Physical Chemistry (context) - Lau, Alper et al. - 1994
1 Saudek and J (context) - Atkinson - 1994
1 Lepage and J (context) - Saudek, Atkinson - 1991
1 Theoretica Chimica Acta (context) - Smith - 1993
1 Journal Of Chemical Physics (context) - White, Headgordon - 1994
1 International Journal Of Modern Physics C Physics and Comput.. (context) - Plimpton, Hendrickson - 1994
1 Atkinson and J (context) - Saudek - 1991
1 Molecular Physics (context) - Petersen, Perram - 1989
1 Computer Physics Communications (context) - Berendsen, Vanderspoel et al. - 1995
1 Computer Physics Communications (context) - Bruge - 1995
1 International Journal Of Modern Physics C Physics and Comput.. (context) - Hedman, Laaksonen - 1993
1 Journal Of Molecular Liquids (context) - Delbuono, Cohen et al. - 1994
1 Mesirov and B (context) - Tamayo - 1991
1 McCammon and L (context) - Clark, van Hanxleden - 1994
1 Computer Physics Communications (context) - Rapaport - 1993
1 for publication in: Proceedings of the SIAM Conference on Pa.. (context) - Plimpton, Pollock et al. - 1997
1 Journal Of Chemical Physics (context) - Luty, Tironi et al. - 1995
1 Computer Physics Communications (context) - Brown, Clarke et al. - 1993
1 Faseb Journal (context) - Lin, Pettitt et al. - 1992
1 Vashishta and S (context) - Kalia, Nakano et al. - 1993
1 Martyna and B (context) - Tuckerman - 1990
1 Acs Symposium Series (context) - Windemuth - 1995
The graph only includes citing articles where the year of publication is known.
Documents on the same site (http://www.incm.u-nancy.fr/Chercheurs/David.Brown/pub.html):
Modelling The Active Site Of Glyceraldehyde-3.. - Cartier, Brown.. (Correct)
Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback
CiteSeer.IST - Copyright Penn State and NEC