Molecular dynamics (MD) simulations follow the motions and interactions of atoms and molecules over time. MD allows investigation of complex systems like fluids, polymers, and proteins. It is commonly used to study phenomena in liquids, solids, soft matter, and astrophysics. Popular MD software packages include GROMACS, CHARMM, AMBER, NAMD, and LAMMPS. While powerful, MD has limitations such as small system sizes and neglecting quantum mechanical effects.