Large scale simulation of parallel molecular dynamics

This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the simulation of molecular dynamics designed to handle large proteins in biology. The implementation is based on the multi-threading parallel programming environment, called ATHAPASCAN which allows to implement and evaluate easily several load-balancing strategies. Some experiments run on one of the largest molecule ever simulated (a hydrated /spl beta/-galactosidase with 413039 atoms) show the interest of such a parallel programming environment.