[georgismilyanov]

It is not simultaneous. I use the Gillespie technique for stochastic simulation. I select a mouse at random to change boxes, depending on its transition rate compared to the transition rate of the system as a whole.

[Someone]

Are the mice interchangeable? If so, can you simulate one, get a distribution of box occupancy from it, and compute interactions from that?

[georgismilyanov]

No. That's the point. It is a simulation of a complex system. The interactions between the mice are everything.