AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed‐memory hypercube computers

Abstract

AbstractA fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long‐range nonbonded Coulomb and Lennard–Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1‐4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed‐memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen‐containing bonds but also all heavy‐atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time‐step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.