How to find displacement of molecules in cell

Hi,

I want to know how to find displacement of molecules in periodic cell with respect to time. I have CO2 molecules with the other polymer in periodic cell, created by amorphous cell. I am attaching an image of displacement of molecules with repect to time from a research paper, i would like to have the same thing. So, can anybody help me with this. 

User-added image
Thanks®ards,
Abdul.