GROMACS version: 2023.2
GROMACS modification: No
Hi all,
I’m looking at water diffusion confined between two surfaces (using SPC water). Perpendicular to the surface, this should converge to a value given by the distance between the two surfaces (marked by the yellow dashed line in these), as you see on the top figure here:
However, in some simulations it just doesn’t converge, like on the bottom figure.
I have obtained the msd values from gmx msd, I have checked the trajectories, they look fine in every other regard, I get the same result when converting the trajectories with the -nojump option and I have checked for appropriate treatment of pbc. The fitting is to the relevant diffusion equation between two impenetrable surfaces. Diffusion parallel to the surfaces is also fine and this doesn’t appear in all of my systems. What could be the reason for this behaviour/how could it be fixed?
Thanks!