Parallel molecular dynamics simulation: Implementation of PVM for a lipid membrane

✍ Scribed by Zhiwu Fang; A.D.J. Haymet; Wataru Shinoda; Susumu Okazaki

• Publisher: Elsevier Science
• Year: 1999
• Tongue: English
• Weight: 892 KB
• Volume: 116
• Category: Article
• ISSN: 0010-4655
• DOI: 10.1016/s0010-4655(98)00089-7

✦ Synopsis

This paper describes a parallel algorithm for Molecular Dynamics simulation of a lipid membrane using the isothermalisobaric ensemble. A message-passing paradigm is adopted for interprocessor communications using PVM3 (Parallel Virtual Machine). A data decomposition technique is employed for the parallelization of the calculation of intermolecular forces. The algorithm has been tested both on distributed memory architecture (DEC Alpha 500 workstation clusters) and shared memory architecture (SGI Powerchallenge with 20 RI0000 processors) for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer consisting of 32 DPPC molecules and 928 water molecules. For each architecture, we measure the execution time with average work load, and the optimal number of processors for the current simulation. Some dynamical quantities are presented for a 2 ns simulation obtained with 5 processors on DEC Alpha 500 workstations. Our results show that the code