A new decomposition strategy for parallel bonded molecular dynamics

Conference · Wed Dec 30 23:00:00 EST 1992

OSTI ID:10147398

Plimpton, S; Hendrickson, B; Heffelfinger, G

A method is described for parallelizing molecular dynamics (MD) simulations by block-decomposing the matrix of bonded and non-bonded force computations. It is particularly useful for organic simulations (polymers, proteins) because unlike spatial-decomposition methods, it requires no geometric information about the simulation domain. Because its communication cost scales as N/{radical}P. rather than N as in the all-to-all broadcast or ring-exchange techniques commonly used in this type of MD simulation, larger numbers of processors can be used effectively, yielding greater parallel speed-ups.

• Research Organization: Sandia National Labs., Albuquerque, NM (United States)
• Sponsoring Organization: USDOE, Washington, DC (United States)
• DOE Contract Number: AC04-76DP00789
• OSTI ID: 10147398
• Report Number(s): SAND--93-0259C; CONF-930331--8; ON: DE93009839
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
360600
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400201
99 GENERAL AND MISCELLANEOUS
990200
ALGORITHMS
CHEMICAL AND PHYSICOCHEMICAL PROPERTIES
CHEMICAL BONDS
COMPUTERIZED SIMULATION
DYNAMICS
INTERATOMIC FORCES
MATHEMATICS AND COMPUTERS
MOLECULES
ORGANIC POLYMERS
OTHER MATERIALS
PARALLEL PROCESSING
PROTEINS