Team:EPF-Lausanne/Theory

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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.
      Lennard jones vdw forces.jpg
    • when electrostatic charges are present, we add the Coulomb force, where Q1, Q2 are the charges and ϵ0 is the permittivity of free space
Coulomb.jpg


  • the bonded interactions: angles, bonds and dihedral angles have to be taken into account
Bonded.jpg


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