An "MD path" is the path or trajectory that a particle follows in MD. if you ran too short, then the molecules have not moved enough. Diffusion is defined as the limiting behavior of the Mean-Squared Displacement (MSD) at long-times. For diffusional processes, the slope must become linear at long times. If you did not reach that regime yet, then you have ran too short.

Slow diffusion might be outside the reach of MD, e.g. very slow diffusion can not be measured using MD. The maximum is probability up to 10^-14 m^2/s.