Under construction!This post is a work in progress. More features and documentation will be added soon.

This post provides an interactive tool for constructing and simulating molecular dynamics configurations in two and three dimensions. You can click within the simulation canvas to place particles, connect them with bonds, assign angle triplets along bonded paths, configure particle/bond/angle types, then export a LAMMPS configuration file or run a live Langevin dynamics simulation. Note that you can modify any of the parameters on-the-fly as the simulation is running, including e.g. the particle, bond, and angle paramters and the type of particle-particle interactions (Lennard-Jones, Weeks-Chandler-Andersen, or harmonic overlap repulsion).

Try it out!

Particle types
Bond types
Angle types
Some suggestions:
  • Assemble a simple Lennard-Jones liquid with particles of different radii (you can use the "Select" tool to copy and paste groups of particles to make this easier).
  • Construct a simple polymer chain by placing particles in a line and then using the "Bond" tool to connect them, then add angular interactions and play around with the bending stiffness. How does the behavior change as you switch from 2D to 3D?

Useful references:

  1. S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117, 1 (1995)

  2. LAMMPS documentation: read_data command, bond_style harmonic, angle_style harmonic