MULTICOLOR ALGORITHMS IN MOLECULAR SIMULATION - VECTORIZATION AND PARALLELIZATION OF INTERNAL FORCES AND CONSTRAINTS

An algorithm is presented by which list-driven computations of internal forces and bond constraints in molecular simulations can be partitioned into independent sub-lists (colours) which contain only mutually independent forces or constraints. These can be evaluated simultaneously which means that they can be easily vectorised and parallelised. The method is not restricted to a particular system, but can be applied to general molecular topologies. It is generic and does not rely on machine-specific hardware or software.