Thank you Axel,
(Yes it is a vmd issue. ) It sounds very helpful and interesting that the trajectory can be outputted unwrapped. If I used the unwrap trajectory, I think the system will be very sparse and keep growing as the simulation runs. (maybe close to this post: [Outputting LAMMPS trajectory file - #2 by akohlmey]).
I want to have a box of the system, but any bonds that span the whole box will be joined. Does the unwrapped output trajectory is what I want in this situation?
Thank you for checking,