How many particles for each kind of particles you would like to simulate?
And what are the size of each kind of particles (or ratio of radius between two particles?)?
What are the average kinetic energy of each kind of particles (the same average kinetic energy or the same average velocity?)

[quote]When there is collision of any of these two kinds of particles, the system stops and scrambles the position of all particles but the counters do not initialize. [/quote]
If there are too many particles , collision between two particles will occurs very shortly.
Do you really want to scrambles the position of all particles ???