analysis of mean square displacement over time

[yugi]

hi there
I have been asked to do "analysis of mean square displacement over time". I have fulfilled my simulations. and, positions (xyz coordinates) of particles over time are recorded. therefore, I know positions of particles in every time-step: (t=0; x0,y0,z0), (t=1ns; x1,y,1,z1), (t=2ns; x2,y,2,z2) and so on.
but i dont know how to do an "analysis of mean square displacement over time" numerically. what to they mean when they ask "analysis of mean square displacement over time"? can anybody help me please? any REFERENCES, PAPER, TEXTBOOK, is highly appreciated.

Moreover, I'm wondering if anybody can help me to have a deep understanding of "mean square displacement (MSD)". I know it is related to diffusion by : <r^2>=4Dt (in 2dimension), but I dont know the meaning of "t" in this formula. is it "time interval" during which the particle travels distance "r"? then how you can plot MSD vs t?