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.