Instructions: drag an atom with your mouse; change a parameter by clicking on it, typing, hit enter
With a high amount of damping and no gravity the atoms settle down quickly into various configurations. Notice that two of the springs are red and the rest green. We can set the length or stiffness of the red springs separately from the green springs. By doing so the molecule becomes asymmetric.
The symmetric molecule (all springs are same length & stiffness) is only stable in the square configuration. (Actually it is possible to get to the configuration with the red atom in the center, but it is very unstable and hard to get to).
If you click the button labelled "red spring length 2.5" this will set the red springs to be shorter than the green springs. This makes the molecule asymmetric. Now there are are 2 stable configurations each with a different energy level.
Click the button labelled "red spring length 2" and the red springs are now very much shorter than the green springs. This causes one of the stable configurations to disappear and there is again only 1 stable configurations.
In the study of dynamical systems, this is known as a bifurcation which means that slowly changing a parameter of the system (the spring stiffness here) causes the number of stable states of the system to change.
The energy is calculated as the sum of the kinetic energy (of motion) and the potential energy stored in springs that are stretched from their resting length (gravity also is a source of potential energy).