Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines

IEEE Computational Science and Engineering

Volumn 2, Issue 2, 1995, Pages 18-29

  Hwang, Yuan Shin ^a   Das, Raja ^a   Saltz, Joel H ^a   Hodošček, Milan ^b   Brooks, Bernard R ^b  

^a UNIVERSITY OF MARYLAND   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; COMPUTER SOFTWARE PORTABILITY; DISTRIBUTED COMPUTER SYSTEMS; EQUATIONS OF MOTION; ITERATIVE METHODS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NATURAL SCIENCES COMPUTING; OPTIMIZATION; PARALLEL ALGORITHMS; SUBROUTINES;

ATOM DECOMPOSITION; CHAOS LIBRARY; COMMUNICATION OVERHEAD; COMPUTATIONAL LOAD; DATA PARTITIONING; DISTRIBUTED ARRAYS; DISTRIBUTED MEMORY MACHINES; FORCE DECOMPOSITION; MESSAGE PASSING LIBRARY; PARALLEL VIRTUAL MACHINE LIBRARY;

PARALLEL PROCESSING SYSTEMS;

EID: 0029322399     PISSN: 10709924     EISSN: None     Source Type: Journal    
DOI: 10.1109/99.388949     Document Type: Article

References (9)

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2. W.F. van Gunsteren and H.J.C. Berendsen, “Gromos: Groningen Molecular Simulation Software,” tech. report, Laboratory of Physical Chemistry, Univ. of Groningen, Nijenhorgh, The Netherlands, 1988.
3. P.K. Weiner and P.A. Kollman, “Amher: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions,” F. Computational Chemistry, Vol. 2, No. 3, 1981, pp. 287–303.
4. B.R. Brooks and M. Hodośček, “Parallelization of Charmm for MIMD Machines,” Chemical Design An-tomation News, Vol. 7, No. 16, 1992, pp. 16–22.
5. T.W. Clark et al, “Parallelizing Molecular Dynamics Using Spatial Decomposition,” Proc. ’94 Scalable High Peiformance Computing Conf., IEEE Computer Soc., Los Alamitos, Calif., 1994, pp. 98–102.
6. H. Sato et al, Parallelization of Amher Molecular Dynamics Program for the API000 Highly Parallel Computer,” Proc. ’92 Scalable High Performance Computing Conf., IEEE Computer Soc., Los Alamitos, Calif., 1992, pp. 113–120.
7. J.H. Saltz et al, “A Manual for the CHAOS Runtime Library,” Tech. Report CS-TK-3437 and UMIACS-TK-95-34, Dept, of Computer Science, Univ. of Maryland, 1995.
8. R. Mirchandaney et al, “Principles of Runtime Support for Parallel Processors,” Proc. 1988 ACM Int’l Conf. on Supercomputing, ACM, New York, 1988, pp. 140–152.
9. S. Plimpton, “Fast Parallel Algorithms for Short-Range Molecular Dynamics,” Tech. Report Sand91–1144, San-dia Nat’l Laboratories, Albuquerque, N.M., May 1993.