I think you mean to ask if you can use COOR ANAL to calculate the lipid diffusion.
There is no assumption about water, but you have to be aware that the MSD calculation is made for each individual atom in the selection (no center-of-mass or other positional averaging is done). It is not clear to me why you don'tn need PBC (support for which is limited in COOR ANAL).

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden