Dear Dr. Nilson and rick
thank you very much for your support.
Actually, my system was simulated under PBC and it is a bilayer system. I observed some of lipids move out of the box, which I expect it should be no problem under PBC. After I combined the trajectory(merge trj), I observed the lipids were recentered in the PBC box, but whole system slightly drift (visualized by vmd)during the period of MD. I assumed that it may be due to wrong removal of center of mass correction. Such that, the diffusion coefficient for my system is very large.
I think perhaps I might need to subtracts the movement of system with certain value. Any comments would be appreciated.