Molecular dynamics method to simulate a simple fluid

Question

I need to implement the molecular dynamics method to simulate a simple fluid that interacts through the Lennard-Jones potential in a 2D simulation. The idea is to explore how the total energy of the system (kinetic + potential) and the particle trajectories depend on the size of the chosen time step.

I took a piece of code that does part of the job(I will upload it here) but I would like a algorithm to helpe-me to finish. I will try to summarize what I understood until now:

1. Initially it sets the physical parameters and parameters of simulation

• temperature
• density
• number of particles
• size of the box
• Lennard-Jones cut-radius
• Verlet-list radius

2. It initializes the vectors and lattice

• position and velocity vectors x,y and vx,vy
• distributes the particles in a square centered lattice
• Chooses velocities uniformly on a unit circle
• Normalizes the velocities according to the energy equipartition theore
• make the total momentum of the particles equal to zero

3. Creates a verlet list to define neighbors

My doubts are:

How and when to use Lennard Jones potential and Verlet Velocities in the code ? Does someone have an example algorithm or can put it in a manner that I can follow the steps?

The code until now: MolecularDynamics_2DfluidSimulation

Answer 1

Based on the comment by Magic_Number and the comment by B. Kelly, and the lack of response, and the OP not signing in for the last 7 months, I'll assume that it's enough to say that this link provided by Magic_Number has the required code, and I'll say that this Community Wiki post can be deleted if someone wants to write a more detailed answer.