1. Simulation can be done with different model. What is important is how make sense of the simulation.
The gravity is the same (-g ) for all particles in the above simulation, because that what phyiscs tell me.

[quote]Ma =29 therefore relative to it's self it has a vertical force of 29/29 upwards and 29/29 downwards. Gas B has a upwards force of Ma/Mb and downwards force of Mb/Ma  and Gas C has a upwards force of Ma/Mc and downwards Mc/Ma.  [/quote]
I do not understand the physics meaning of your model:
1. What do you mean by upward force and downward force?
If particle A has the same upwards and downwards force, the net force is zero. Then, particle should move with constant velocity.
2. Why the download forces and upwards force are different for particle B/C?
3. Do you mean force or acceleration?

The temperature range can be change easily. However, the value of temperature slider (T) was used to calculate the initial average velocity for all the particles. It is not the real temperature when it reach equilibrium later on. In order to visualize the effect you want, the gravitation energy was set to a much larger value (compared to real gas under STP condition).

If you just want to have three different gas particles moving in different layer, it can be generated, too! However, it is far from real!

Do you really want to simulate some physical model you have?
Or you just want to have some visualized effect?
Are you using it for teaching purpose? What is the purpose to have such simulation?

For real gas:
The separation between gas particles are much larger than the size of the particles.
And there are 10[sup]19[/sup] particles in 1 cm[sup]3[/sup].

A good model need to be designed properly to simulate real gas.