Basic MD algorithm#

Lennard-Jones

Fig. 8 MD flowchart.#

Algorithm 1 (Basic Molecular Dynamics Algorithm)

  1. Define variables, etc. for the calculations

  2. Read in the parameters for simulations (time step, the number of time steps, temperature, etc.)

  3. Initialize the system (read data or generate): Initial values for \(\vec{r}_i\) and \(\vec{v}_i\)

  4. Time loop: Loop over the total number of time steps.

    1. compute forces

    2. Integrate the equations of motion using a numerical algorithm

    3. Save data at a predefined interval or/and compute qunatities

  5. Stop.