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data.in		simulation
nbiter 100 dt 0.01 record 50 boxsize 10 10 cxmax 1 cxdiff 20		click to animate ! download data.in

Above left is a minimal parameter file. In this case, the simulation contains only one object, a motor complex. The outcome of the simulation can be seen by clicking on the picture on the right. The complex is freely diffusion inside a empty box.

• nbiter 100 tells the simulation to perform 100 iterations
• dt 0.01 sets the time step to 0.01 seconds.
  Hence the complete simulation runs on 100 * 0.01 = 1 seconds.
• record 50 tells the simulation to record 50 frames.
  This is done at equal intervals, so in this case every 1 seconds / 50 = 0.02 seconds.
• boxsize 10 10 defines the dimension (w, h) of the box in micrometers,
  the total box is actually 2*w wide, and 2*h high with the origin in the center
• cxmax 1 defines the number of motor complexes,
  cx is short for complex, and max stands for maximum number...
• cxdiff defines the diffusion coefficient of the complexes in micrometers square per seconds.

You can run a similar simulation simply by dowloading the file data.in on your own computer, by clicking on the link below the animation. (see here for instructions on installing and running the program).