Run: Clicking on the Run button starts or resumes Run mode. Run mode is the simulation mode. In the Chemistry Reactor simulator, the Substance Reactor and Particle Reactor combine elements. In the Chemistry Analyzer simulator, the Substance Analyzer and Particle Analyzer decompose compounds. In both simulators, the thermal container heats or cools the substance in the container until it evaporates or freezes, or until the simulation is stopped.

The reactors and analyzers operate instantaneously. Only the heating or cooling of the thermal container keeps running beyond the first second of the simulation. Depressing the Pause button only suspends the the heating or cooling; it does not halt it. Clicking on the Run button while in Pause mode resumes the heating or cooling; it does not restart it.

In Run mode, you cannot access the Standard Menu. You cannot open the Properties Box of the thermal container (except by selecting it and typing control-O). In all other regards, you have access to the same capabilities of the simulators in Run Mode that you do in Stop Mode. However, to run the analyzers or reactors again, you need to click Stop and then click Run again.