# Team:EPF-Lausanne/Theory

### From 2009.igem.org

*Molecular dynamics theory*

Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy. This potential energy can be divided into:

## the non-bonded interactions:

- The
*Lennard-Jones potential*is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms.

- when electrostatic charges are present, we add the
*Coulomb force*, where Q1, Q2 are the charges and ϵ0 is the permittivity of free space

## the bonded interactions:

Angles, bonds and dihedral angles have to be taken into account

To understand a bit more, you can see the following article:
Introduction to Molecular Dynamics Simulation - Michael P. Allen