Press "Reset" to reset the positions and velocities of the molecules to random values. Pressing "Reset to Equal" will cause the velocities to all be the same, although they won't stay that way for long. "Reset to Extreme" will reset half the molecules to a single large velocity and the other half to a small velocity; again, they won't stay that way for more than a fraction of a second. "Set Wall Temp" will set the temperature of the walls to be the same as that of the heater.
The volume slider controls the volume of the container. The Heater Temperature slider controls the heater at the bottom of the screen; if the temperature is high, the heater is more likely to give a large kinetic energy boost to molecules that hit it. If the temperature is low, the heater becomes a refrigerator; it removes kinetic energy from the system. The gravity slider controls gravity.
At the bottom of the screen is a velocity histogram showing the distribution of velocities of the molecules. Again, color is used to indicate velocity; velocities increase as you go to the right on the graph. The height of the velocity bars shows the number of molecules that have that velocity. The scale of the graph changes constantly so watch the colors to orient yourself.