When you hit the green light, the simulator constantly performs this set of calculations, over and over again, moving the planets at every step. If the paths of any two objects overlap, they have collided and the objects are blended into a single planet. The simulator makes some simplifying assumptions. This keeps the calculations simpler and makes the display much easier to handle. The simulator also makes no attempt to incorporate any notion of real time.
Acceleration is the change of location per second per second.
The simulator just assumes that the time it takes to make one pass through its calculations is exactly 1 second, which eliminates a lot of divisions. In reality, the simulator can perform hundreds of steps every second. Neither of these assumptions harms the simulation in any way. You will still get a sense of how objects are affected by gravity. Just don't try to launch the Space Shuttle based upon its findings.