Molecular dynamics (MD) is the act of simulating physical movements of atoms and molecules with computer methods. The atoms and molecules interact in a fixed period of time, which a view of the dynamic evolution of systems can be extracted in this time. In the most common cases, the trajectories of atoms and molecules are determined by numerically solving Newton’s equations of motion in a system of interacting particles. In these systems, forces between the particles and their potential energies are calculated using interatomic potentials or molecular mechanics force fields. Although this method was originally developed within the field of theoretical physics in the late 50s, today it has a vast range of use mostly in chemical physics, materials science and the modeling of biomolecules.
Because molecular systems typically consist of abundant particles, it is almost impossible to analytically determine the properties of such systems; MD simulation is an alternative method to solve this complexity by using numerical methods.
On the other hand, in many cases, MD simulations end up generating many errors. This errors have a mathematical base and require a knowledge to properly select algorithms and parameters.
MD group of Sharif Upstream Petroleum Research Institute aim to start a long program in this fabulous area. We believe that by studying the basic behaviour of molecules in a very small scale, it is possible to create more methods in engineering, especially in the field of oil and gas to maximize the operations.