COOR ANAL can handle PBC with orthogonal lattice types, but only computes MSD for single atoms, not the molecular COM.

I see.

By "small", I meant less than ten or so lipids; your system seems okay.

Note that since there is both a short time and long time diffusion, one must care in the fitting to discard either the short time or long time data. Plots of r^2 vs t, esp. averaged over molecules, should make it clear where the slope change occurs.

I am interested in the long time diffusion so I'll drop the short time data. Mhhh, well thinking twice about it, I am probably interested in both parts so I have to calculate it twice

Also i will cut my simulation into some larger parts and calculate the diffusion only for these parts to compare them against each other.

Thanks for the notes.

Kind regards

Bjoern