title: Mean square displacement python
body: <p>I have a trajectory file from simulation of 20,000 frames with 5 ps time in between every frame, what I want to do is to calculate diffusion in 2 dimension (x and y axis). but to calculate diffusion in 2D, first I have to calculate Mean square displacement of the molecule under study. MSD calculates the average time taken by molecule to explore the system in random walks. </p>
  
  <p>I am very new to python programming and I would really want some help to get started this problem and to solve this problem. Hope to get positive response. </p>