Team:EPF-Lausanne/Theory

From 2009.igem.org

Revision as of 07:24, 8 September 2009 by Guittet (Talk | contribs)

Contents


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

Lennard-Jones pair potential showing the r−12 and r−6 contributions
  • 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


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


Back to top