A HIGHLY PORTABLE PARALLEL IMPLEMENTATION OF AMBER4 USING THE MESSAGE-PASSING INTERFACE STANDARD

We have implemented a portable parallel version of the macromolecular modeling package AMBER4. The message passing paradigm was used. All me ssage passing constructs are compliant with the Message Passing Interf ace (MPI) standard. The molecular dynamics/minimization module MINMD a nd the free-energy perturbation module Gibbs have been implemented in parallel on a number of machines, including a Gray T3D, an IBM SP1/SP2 , and a collection of networked workstations. In addition, the code ha s been tested with an MPI implementation from Argonne National Laborat ories/Mississippi State University which runs on many parallel machine s. The goal of this work is to decrease the amount of time required to perform molecular dynamics simulations. Performance results for a Lip id bilayer molecular dynamics simulation on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995 by John Wiley & Sons, Inc.