I will discuss some computational aspects in molecular dynamics simulations: including modeling of atomic interaction, time integration, averaging, isothermal simulations (thermostating) and boundary conditions. Ref.  D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, second edition.  X. Li and W. E, Boundary conditions for molecular dynamics simulations of solids at low temperature, Comm. Com. Phys., 1 (2006), 136--176. .