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-pass ing paradigm is adopted for interprocessor communications using PVM3 (Paral lel Virtual Machine). A data decomposition technique is employed for the pa rallelization of the calculation of intermolecular forces. The algorithm ha s been tested both on distributed memory architecture (DEC Alpha 500 workst ation dusters) and shared memory architecture (SGI Powerchallenge with 20 R 10000 processors) for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer consisting of 32 DPPC molecules and 928 water molecules. For each architec ture, 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 Alph a 500 workstations. Our results show that the code is extremely efficient o n 5-8 processors, and a useful addition to other major computational resour ces. (C) 1999 Published by Elsevier Science B.V.