This chapter is aimed towards understanding damage progression and failure in advanced nanostructured composite materials. The molecular dynamics (MD) program LAMMPS (large-scale atomic/molecular massively parallel simulator) is a versatile code with numerous functionalities which can be used to simulate polymer systems. Although the results for molecular simulation models, in particular polymer models, are system size dependent, the ease with which large molecular systems can be evaluated, especially with parallel molecular dynamics codes such as LAMMPS, makes it a more attractive choice compared to other approaches such as ab initio calculations, which are limited to the calculation of a few 100 atoms.