Atomistic simulations of two isomers of polybutadiene (PB), cis-1,4-PB and 1,2-PB, have been conducted using the end-bridging Monte Carlo algorithm. The maximum mean molecular lengths of the polymer chains were C-1000 and C-161 for cis-1,4-PB and 1,2-PB, respectively. The simulated ensembles of configurations were evaluated in terms of equilibration rate and conformational, volumetric, and structural properties. The results illustrate the correlation between successful end-bridging, reptation, and concerted rotation (CONROT) moves and the enhanced equilibration rate of large systems with long chains. Comparison with experimental data shows that the simulations underestimate the specific volume to some extent, especially for 1,2-PB. Simulation predictions for the torsion angle distribution, end-to-end distance, radius of gyration, and characteristic ratio are in good agreement with experiment, confirming the ability of the force field to reproduce the structure of real PB melts. Analysis of geometric features of the pure component intermolecular pair distribution functions is applied to gain insight about miscibility in polybutadiene/polyisoprene binary blends.