Large Scale Simulation of Parallel Molecular Dynamics

This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the sim-ulation of molecular dynamics designed to handle large proteins in biology. The implementation is based on the multi-threading parallel programming environment, called ATHAPASCAN 1 which allows to implement and evaluate easily several load-balancing strategies. Some experiments run on one of the largest molecule ever simulated (an hy-drated-galactosidase with 413039 atoms) show the inter-est of such a parallel programming environment