The bonding geometry at the metal molecule interface plays an important role in determining the conductance behavior of metal molecule metal junctions. This bonding geometry has to be determined a priori in quantum mechanical current voltage (I-V) calculations. To identify the detailed metal molecule bonding configurations, we perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) to explore the dynamic elongations of gold nanowires in the presence of benzenedithiol (BDT) molecules. A specific multitime-scale double reversible reference system propagator algorithm (double-RESPA) has been designed for the metal organic complex in MD simulations to improve the simulation efficiency. We investigate the variations of bonding sites and bonding angles of BDT molecules on a stretched Au nanowire at a constant chemical potential. The density of BDT and the number of bonded and nonbonded BDT molecules in the simulation box is monitored during the entire elongation process. Simulation results show that BDT molecules can form a denser monolayer on Au nanowires than at the Au (111) surface, owing to the many atomic steps on curved surfaces. Moreover, the chemical bonding of BDT on the Au nanowire significantly effect the elongation behavior of Au nanowires compared with those in vacuum. Our present results will be valuable to the understanding of the broken junction mechanism in molecular electronics conductance measurements.