Run: Clicking on the Run button starts or resumes Run mode. Run mode is the simulation mode and the only mode in which physics works at both the macroscopic and microscopic levels. Particles move, solids melt, liquids freeze or evaporate, and gases diffuse only during Run mode. Cannons, heater/coolers, gas tanks, vacuum pumps, and pistons only function in Run mode. Meters operate in both Stop mode and Run mode.

Depressing the Pause button only suspends the simulation; it does not halt it. Clicking on the Run button while in Pause mode resumes the simulation; it does not restart it.

Depressing the Stop button not only halts the simulation, it resets the simulation to the initial state. Because you can change the simulator setup during Run mode, this "initial state" may or may not correspond to the simulator state at time zero.

Starting a simulation from Stop mode always starts the clock, which only functions during Run mode. Resuming a simulation from Pause mode restarts the clock from the paused time. Clicking on Stop resets the clock to zero.

In Run mode, you cannot access the Standard Menu. Other than that, you can interact with the simulator and its elements and objects as completely in Run mode as you can in Stop mode.