If the lipids were subject to image centering during the simulation, then you must account for that; but that's not the biggest problem.

I don't believe COOR ANAL is suitable for lipid diffusion. The rigorous approach to compute diffusion is to use the center-of-mass (COM), and for lipids, that's often done as a 2D diffusion, not 3D. COOR ANAL is not set up to use the COM to compute r^2 vs t, or to compute r in 2D instead of 3D.

Also, coupling between neighbors leads to size effects; see

Dynamical motions of lipids and a finite size effect in simulations of bilayers
Jeffery B. Klauda, Bernard R. Brooks, and Richard W. Pastor
J. CHEMICAL PHYSICS 125(14) Article No. 144710 (2006)

See also this thread

Note that the finite size correction discussed in that thread only applies to cubic systems at present, and would not help with the coupling problem.


Rick Venable
computational chemist