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A new parallel method for molecular dynamics simulation of macromolecular systems
Author(s) -
Plimpton Steve,
Hendrickson Bruce
Publication year - 1996
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199602)17:3<326::aid-jcc7>3.0.co;2-x
Subject(s) - computer science , molecular dynamics , parallel computing , computation , benchmark (surveying) , range (aeronautics) , speedup , parallel algorithm , computational science , algorithm , chemistry , computational chemistry , materials science , geodesy , composite material , geography
Short‐range molecular dynamics simulations of molecular systems are commonly parallelized by replicated‐data methods, in which 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 interprocessor communication scales as N (the number of atoms) independent of P (the number of processors). Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this article a new parallel method for simulating macromolecular or small‐molecule systems is presented, called force‐decomposition. Its memory and communication costs scale as N /√ P , allowing larger problems to be run faster on greater numbers of processors. Like replicated‐data techniques, and in contrast to spatial‐decomposition approaches, the new method can be simply load balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024‐processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y‐MP processor. © 1996 by John Wiley & Sons, Inc.