Every molecule feels two things at once: a faint pull when a neighbour drifts near (the van der Waals attraction) and a hard shove if it gets too close. Drawn against distance, those two make a shallow well — the Lennard-Jones potential you are running here.
Temperature is just how hard the molecules jiggle. When the jiggling beats the well, they tear free and fill the box — a gas. When the well wins, they cling into a liquid drop, and colder still they settle into the repeating solid lattice.
Turn the well deeper — stronger forces — and it takes more heat to shake the molecules loose, so the melting and boiling points climb. That is why water, held by strong hydrogen bonds, boils at 100°C while methane, held by the weakest forces, boils at −161°C. The dashed gold lines on the thermometer are this lab's honest guess at where this well melts and boils; watch them rise as you deepen it.
This is a real molecular-dynamics simulation — the same velocity-Verlet method chemists use to model proteins and new materials, just small enough to watch.
The simulation stopped unexpectedly — the lesson continues without it. You can move on; nothing you did was wrong.