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I have performa 500 ps simulation of just the water molecules (SPC) model. Towards the end I can see a curve. I am unable to understand the reason behind it. can anyone explain ?
I would say that 100 water molecules and 500ps are both a very limited number of molecules and a very short time. You should have a longer run with many more molecules, as I can’t even think about how can 100 molecules fit in a box without PBC artifacts.
Then probably you have your answer: you need more statistics to get a better MSD estimate! :)
I might be wrong, but also I think the associated error to your diffusivity from the MSD you plot is going to be small even with the kind. Nevertheless, the more statistics the better.
The MSD curves tend to be noisier as time increases since the variance in molecule displacement becomes higher (there is more time for molecule pathways to diverge in the chaotic system), so that’s why you get the noise at the end of the curve. As previously discussed in this post, including more water molecules in your average should get rid of the bump.