I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to interpret MSD results, I would be grateful.
I have been running NPT simulations to collect data for use in fluid dynamics simulations. However, I now realize that I have used low temperatures compared to people who have looked at similar systems. So I want to evaluate MSDs to make sure the simulations are ergodic.
I don't have much experience with statistics and a basic point I don't understand is whether it is the slope of the MSD or the R value that matters. Or both.
An example of an MSD I have calculated is below. I get this output (I can't control the time interval used, the software chooses it):
Linear regression interval 41.52 - 83.03 ps. MSD(t) = -10806.283111 + 1575.888517 * t R = 0.977891
When I calculate a slope on the interval 1 ps to where the curve goes vertical, I get ~0.8, which I know is not great. I don't know what an acceptable value would be but am guessing >0.9. I do get 0.95 if I calculate the slope not from 1 ps, but from 10 ps. But on a log-log plot, that's a small interval. Is it unacceptably small?