Parallel molecular dynamics simulation: implementation of PVM for a lipid membrane
This paper describes a parallel algorithm for Molecular Dynamics simulation of a lipid membrane using the isothermal-isobaric 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 dusters) and shared memory architecture (SGI Powerchallenge with 20 R10000 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 is extremely efficient on 5-8 processors, and a useful addition to other major computational resources. (C) 1999 Published by Elsevier Science B.V.
pvm lipid simulation parallel and distributed processing