What is Molecular Dynamics?
By means of a molecular dynamics simulation, one tries to calculate molecule or substance properties on the computer in order to make predictions for the real world. This can be, for example, the determination of the melting temperature.
How does a Molecular Dynamics Simulation Work?
The basis of molecular dynamics simulations is the calculation of forces between individual particles. Often the atoms are used as elementary particles and now one calculates the forces between the individual particles. Since atoms have electrons, there is a repulsion between atoms that are very close to each other, also called Pauli repulsion. If one really wants to calculate this exactly on a quantum mechanical level, this is very complex. Therefore, pseudopotentials are often used. These are simple mathematical functions, which are very similar to the real forces. One such function is the Lennard Jones potential.
The lennard-jones potential, Source
Now this potential and the Netwton equations can be used to determine how the atoms move relative to each other.
Image of a simple Molecular Dynamics simulation, source
Limitations of Molecular Dynamics Simulation
Molecular dynamics simulations simulate very small time spans. It is not possible to simulate processes that last a few seconds. Instead, the processes simulate only picoseconds. So for such processes one needs other procedures.