I am trying to calculate lateral lipid diffusion via simulation in the xy direction . The method I used to calculate the diffusion is by calculating the gradient or slope of plot of MSD (mean square displacement) vs (time).
Here I attached a plot I got for MSD vs time.
But the plot I got shows some negative gradient or slope in the middle of the graph.
How one can explain this kind of plot?
I have some doubts if the plot is correct? Ask
Appreciate if I can get some guidance here.
note: ( I used AMBER to simulate my system)