PARALLEL MOLECULAR-DYNAMICS OF BIOMOLECULES

The basic principles of a typical sequential Molecular Dynamics (MD) program suitable for the study of solvated biomolecules are described, the inherent parallelism of MD is analysed and strategies for parallelisation are developed. Due to separate treatment of computation and communication a high level of portability is achieved and both tasks can be optimized independently. It is found out that communication trees are highly efficient means for sending, receiving and gathering the computed data, especially for large processor numbers. A current implementation on a transputer system is presented, Due to the tight memory budget slight modifications are necessary. Nevertheless, we get excellent performance with an average degree of parallelization of 82%.