Before starting the simulation, the program cytosim reads the file config.cym. This tutorial will explains you all the parameters that you can specify in config.cym and their meaning, in 30 easy steps. An example is given at every page, which you can view by clicking on the picture. In parallel, you should download the file config.cym and run a similar simulation on your computer, fiddling with the parameters if you want.
Cytosim only understands plain text files, so you should edit config.cym with a plain text editor (TextEdit on macs) rather than e.g. MS-Word. config.cym should usually be in the same directory as cytosim.