Molecules 3D simulates the interaction of charged
particles in three dimensional space. The particles
interact via the classical Coulomb force, as well as
the repulsive quantum-mechanical Pauli force, which
acts at close distances (accounting for the "collisions"
between them). The motion of the particles is also damped
by a term proportional to their velocity, allowing them
to "settle down" into stable (or meta-stable)
Moving in response to these forces, the particles will
eventually end up in a configuration of minimum potential,
where the net force on any given particle is essentially
zero. Generally, individual particles will first pair
off into dipoles and then slowly combine into larger
structures. Rings and straight lines are the most common
configurations, but by manipulating particles manually,
they can be coaxed into more complex meta-stable formations.
Additionally, pressing "w" will toggle the
presence of potential well directed radially inward
toward the center of the 3d space. This can be used
to bring the particles closer to one another if they
start to drift apart.