Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system.
In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton’s equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules.
Lammps is one of the popular simulation packages that we will discuss about.
3D Model of 5ENL (PDB ID from rcsb PDB)