What if you already have your own mobility simulation, but are missing the agent optimization / re-planning part? Well, you can use your own mobility simulation together with MATSim as long as you are able to read in our plans and network and generate events.
The external mobility simulation will be called with a configuration file as its only argument. In the con¬figuration file, you find parameters describing the location of the network file, the location of the plans file, and the location of the events file. Your mobility simulation should read network and plans and generate events.
We provide for testing reasons a very simple example of an external mobility simulation that just out¬puts a few hard-coded events. You can run the example with:

java -cp MATSim_r4776.jar org.matsim.run.Controler examples/tutorial/externalMobsim.xml

Have a look at the configuration file to understand how the run is configured to use the external mobsim.
If you intend to write your own mobility simulation, please read the documentation about events in the Developer’s Guide (http://www.matsim.org/docs/devguide). The events are a very important aspect in MATSim as they provide feedback from the mobility simulation to the re-planning parts of MATSim. Without (or with wrong) feedback from the mobility simulation, no useful re-planning is possible.