Parallel Computer Simulation Techniques for the Study of Macromolecules

Abstract

This article will review some of the progress made recently in developing parallel simulation techniques for macromolecules. It will start with simple methods for molecular dynamics, involving replicated data techniques; and go on to show how parallel performance can be improved by careful load-balancing and reduction of message passing. Domain decomposition MD methods are then presented as a way of reducing message passing further, so that effective parallelisation can occur with even the slowest of communication links ethernett). Finally, parallel techniques for conducting Monte Carlo are reviewed, and ways of combining parallel methods are presented. The latter looks like becoming an effective way of using massively parallel architectures for macro-molecules, without the need to simulate huge systems sizes.