I need to calculate the translational diffusion of bulk water for T=300K and P = 1atm. Does anyone have a tutorial explaining how to calculate the translational diffusion via lamps or MSD via post-processing?

I need it to answer a referee and I never calculated it.

There are several ways of doing so and LAMMPS manual has a dedicated how-to section as well as dedicated examples and several discussions archived on the forum.

Adapting a script from the examples to use msd/chunk instead of msd to compute the diffusion constant of water molecules should be rather straight forward.

As an alternative to @Germain 's excellent answer, in this case I would often export the trajectory into a NumPy data structure with MDAnalysis and directly process the coordinates as numbers-over-time.