A new parallel method for molecular dynamics simulation of macromolecular systems

S Plimpton and B Hendrickson, JOURNAL OF COMPUTATIONAL CHEMISTRY, 17, 326-337 (1996).

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/root 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 Gray Y-MP processor. (C) 1996 by John Wiley & Sons, Inc.

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