compute MSD

I try to calculate MSD for water molecules then i use compute msd command .When I use water molecules as group ID the results that i get are very different from the time that I use oxygen atoms as group ID , Can you please let me know why ?
If I want to present water MSD which way is better to calculate : with water group ID or oxygen atoms ?

compute 1 water msd or compute 1 oxygen msd

Thanks for your attention.

Just O atoms should be fine. If your “water” group includes O and H atoms
then in the limit of a long run (lots of diffusion), the answers can’t
be that different. Also make sure you start the simulation
with correct image flags in your data file if any of the water molecules
overlap a periodic boundary. If you don’t do that, your MSD will be


Thank you for the clarification.