A highly portable parallel implementation of AMBER4 using the message passing interface standard

✍ Scribed by James J. Vincent; Kenneth M. Merz Jr.

• Publisher: John Wiley and Sons
• Year: 1995
• Tongue: English
• Weight: 673 KB
• Volume: 16
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540161110

✦ Synopsis

We have implemented a portable parallel version of the macromolecular modeling package AMBER4. The message passing paradigm was used. All message passing constructs are compliant with the Message Passing Interface (MPI) standard. The molecular dynamics/minimization module MINMD and the free-energy perturbation module Gibbs have been implemented in parallel on a number of machines, including a Cray T3D, an IBM SPl/SP2, and a collection of networked workstations. In addition, the code has been tested with an MPI implementation from Argonne National Laboratories/Mississippi State University which runs on many parallel machines. The goal of this work is to decrease the amount of time required to perform molecular dynamics simulations. Performance results for a lipid bilayer molecular dynamics simulation on a Cray T3D, an IBM SPl/SP2, and a Cray C90 are compared.