Before starting the simulation, the program cytosim reads the file data.in to find values for its parameters. This tutorial will explains you all the parameters that you can specify in data.in, and their meaning. This is done step by step, in 40 easy pages. An example is given at every page, which you can view by clicking on the picture. In parallel, you can download the file data.in and run a similar simulation on your computer, fiddling with the parameters if you want.
Cytosim only understands plain text files, so if you edit data.in with e.g. MS-Word, dont forget to save it as a plain text file! data.in should also be in the current directory.