THE OBJECT-ORIENTED DEVELOPMENT OF A PARALLEL APPLICATION IN PROTEIN DYNAMICS - WHY WE NEED SOFTWARE TOOLS FOR HPCN APPLICATIONS

We analyse the concurrency and performance of the various types of for ce calculations involved in the molecular dynamics simulation of large protein or polyelectrolyte molecules. Although this analysis can in p rinciple be used to write a meta-program to optimize load-balancing of this application on an MPP system, we argue that it is an enormous un dertaking not appropriate for the computational scientist. Instead we argue that it is better to exploit research in parallel execution envi ronments which provide automatic load-balancing for concurrent Object- Oriented applications. We also argue that use of Object-Oriented techn ology in the design of simulation software encapsulates the natural co ncurrency of the system, We illustrate this point with a discussion of the constraint force calculation for a polymeric molecule.