About the Simple Molecules model

A computational simulation of a collection of neutral atoms with the forces between the atoms modeled with both the Lennard-Jones Potential which models Pauli repulsion at short ranges and the attractive van der Waals forces that act over longer-ranges as well as Coulomb forces which describe the forces between atoms of diferent charges.

You can select how many molecules to use and what the temperature should be. The model will automatically stop after 50 nano-seconds of model simulation time (5000 model-steps). When you lower the temperature molecules will group together and freeze into a solid-like state. Increase the temperature to change the state to a gas. Somewhere in between the behavior of the molecules are more like a liquid.

Charges of +1 or -1 are evenly distributed among the atoms. When the Coulomb particle force interaction checkbox is enabled atoms with the opposite charges experience an attractive force. Atoms with similar charges experience a repulsive force. Atoms with a positive charge appear green, atoms with a negative charge appear red.

About the Lennard-Jones potential graph

The Lennard-Jones potential is a simple model describing the forces between a pair of neutral atoms or molecules. When two atoms are very close there is strong repulsion, a little further away the forces are zero, just a bit further there is a weak attraction that then drops as the atoms move further apart.

In the graph above you can change two parameters of the Lennard-Jones equation modeling these forces by either changing the depth of the potential well by dragging epsilon up and down or changing the zero point for the potential by dragging sigma left and right.

User Interface

Only the last 1000 model steps are saved.

References:

Wikipedia: Lennard-Jones Potential

The three different graphs and the molecular visualization use the html5 visualization framework: d3.js