One of the best ways to learn how to use a new tool is to look at examples. The examples given in this manual were adapted from real-life MMTK applications. They are also contained in the MMTK distribution (directory "Examples") for direct use and modification.
The example molecules, system sizes, parameters, etc., were chosen to reduce execution time as much as possible, in order to enable you to run the examples interactively step by step to see how they work. If you plan to modify an example program for your own use, don't forget to check all parameters carefully to make sure that you obtain reasonable results.
The files LangevinDynamics.py and MMTK_langevinmodule.c implement a simple integrator for Langevin dynamics. It is meant as an example of how to write integrators etc. in C, but of course it can also be used directly.