Molecules in Motion: The Basic Idea Behind Dynamic Simulations

Odyssey’s simulations are very different from the simulations you may have encountered in other science media products. The motion of molecules does not arise because a human designer used a software tool to create an animation. Instead, Odyssey uses the basic laws of nature in order to represent molecular matter. The motion of molecules is an outcome of applying these laws, very much like the forces of gravity determine how the planets in the solar system move. In short, there is no "movie" file anywhere in Odyssey.

When you watch a simulation of liquid water in Odyssey, the computer is calculating "time steps". (The program actually makes several steps between screen updates.) The steps are separated by approximately one picosecond of physical time — a very short time indeed! Typically, the computer calculates several thousand time steps during a simulation (up to hundreds of thousands of steps for some systems). Each frame also calculates:

• Intermolecular attractive energy: an energy term that represents van der Waals forces (dispersion forces) between non-bonded atoms.
• Intermolecular repulsive energy: a steeply repulsive energy term for steric interactions at short distance that makes a close "overlap" of non-bonded atoms very unlikely.
• Coulomb energy (both inter- and intramolecular): energy term due to the assignment of "effective charges” to all the atoms of a molecule; at the intermolecular level, this energy represents charge-charge, charge-dipole, and dipole-dipole interactions

As you can see, there's a lot going on in each rendered frame. This explains why Odyssey provides such engaging scientifically sound molecular simulations.