PVM-AMBER - A PARALLEL IMPLEMENTATION OF THE AMBER MOLECULAR MECHANICS PACKAGE FOR WORKSTATION CLUSTERS

A parallel version of the popular molecular mechanics package AMBER su itable for execution on workstation clusters has been developed. Compu ter-intensive portions of molecular dynamics or free-energy perturbati on computations, such as nonbonded pair list generation or calculation of nonbonded energies and forces, are distributed across a collection of Unix workstations linked by Ethernet or FDDI connections. This par allel implementation utilizes the message-passing software PVM (Parall el Virtual Machine) from Oak Ridge National Laboratory to coordinate d ata exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid bilayer systems indicate tha t reasonable parallel efficiency (70-90%) and computational speedup (2 -5 X serial computer runtimes) can be achieved with small workstation clusters (typically six to eight machines) for typical biomolecular si mulation problems. PVM-AMBER is also easily and rapidly portable to di fferent hardware platforms due to the availability of PVM for numerous computers. The current version of PVM-AMBER has been tested successfu lly on Silicon Graphics, IBM RS6000, DEC ALPHA, and HP 735 workstation clusters and heterogeneous clusters of these machines, as well as on CRAY T3D and Kendall Square KSR2 parallel supercomputers. Thus, PVM-AM BER provides a simple and cost-effective mechanism for parallel molecu lar dynamics simulations on readily available hardware platforms. Fact ors that affect the efficiency of this approach are discussed. (C) 199 5 by John Wiley & Sons, Inc.