These two MSD are based on the same trajectory and same original frame.

The only difference is that the second one has extra 1 ns.

If the MS calculate the MSD by the formula of

https://community.accelrys.com/servlet/JiveServlet/showImage/2-14120-12429/MSD.JPG

, the first graph should be part of the second graph.

However, it seems not. The height and location of peak looks different.

It looks like the reference frame is different, but I have checked that I set both the original frame to 1 and the length to the last frames.

I have refered to the previous discussion whereas I still do not understand how MSD is calculateed in materiald studio.

I will really appreciate if someone can tell me about how it works.