The virtual system and the sequence of actions to be performed must be given in a configuration file (e.g. config.cym). It contains commands and definitions of objects with parameters. The config file should be a plain text file and it can be edited by any plain text editor.

You will at least want to:

call set to define new objects categories,
call new to create objects,
call run to perform simulation steps.

Most commands accept parameters, and there are many objects to choose from.

For more details, please check:

Example

% A confined fiber
% F. Nedelec, April 2010
set simul fiber 
{
    time_step = 0.005
    viscosity = 0.02
}
set space cell
{
    geometry = ( sphere 5 )
}
new space cell
set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 200
}
new 1 fiber microtubule
{
    length = 12
}
run 5000 simul *
{
    nb_frames = 10
}

For more examples, check the Tutorial and see the Collection of Config Files.