Yuan-Shin Hwang, Raja Das, Joel Saltz, Bernard Brooks, Milan Hodo Scek  Home/Search
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Abstract: CHARMM (Chemistry at Harvard Macromolecular Mechanics) is a program that is widely used to model and simulate macromolecular systems. CHARMM has been parallelized by using the CHAOS runtime support library on distributed memory architectures. This implementation distributes both data and computations over processors. This data-parallel strategy should make it possible to simulate very large molecules on large numbers of processors. (Update)
Context of citations to this paper: More
.... better than atom decomposition by reducing communication costs through the use of a block decomposition, as in LAMMPS [13] and CHARMM [6], and as discussed in reference [12] d) Spatial decomposition, which uses linked lists and scales very well, but it is more difficult to...
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BibTeX entry: (Update)
Y.-S. Hwang, et. al. Parallelizing molecular dynamics programs for distributed memory machines. IEEE Comp. Sci. and Engr., pages 18--29, Summer 1995. http://citeseer.ist.psu.edu/hwang94parallelizing.html More
@article{ hwang95parallelizing,
author = "Yuan-Shin Hwang and Raja Das and Joel H. Saltz and Milan Hodoscek and Bernard R. Brooks",
title = "Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines",
journal = "IEEE Computational Science \& Engineering",
volume = "2",
number = "2",
month = "Summer",
pages = "18--29",
year = "1995",
url = "citeseer.ist.psu.edu/hwang94parallelizing.html" }
Citations (may not include all citations):120 Charmm: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
79 Principles of runtime support for parallel processors (context) - Mirchandaney, Saltz et al. - 1988 ACM DBLP
57 Fast parallel algorithms for short-range molecular dynamics - Plimpton - 1993 ACM
31 Parallelization of charmm for mimd machines (context) - Brooks, Hodoscek - 1992
29 Parallelizing molecular dynamics using spatial decomposition - Clark, Hanxleden et al. - 1994
15 Parallelizing molecular dynamics codes using the Parti softw.. - Das, Saltz - 1993 DBLP
14 Amberassisted model building with energy refinement (context) - Kollman, model et al. - 1981
8 Value-based distributions in fortran d --- a preliminary rep.. - Hanxleden, Kennedy et al. - 1993
7 Gromos: Groningen molecular simulation software (context) - van Gunsteren, Berendsen - 1988
5 Supporting irregular distribution FORTRAN DHPF compiler - Yuan, Joel et al. - 1994
4 Programming abstractions for run-time partitioning of scient.. (context) - Baden - 1987 ACM DBLP
3 Available via anonymous ftp directory hyena (context) - Saltz, for et al. - 1993
The graph only includes citing articles where the year of publication is known.
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