Atoms still out of box after wrapping the coordinates


I do methane hydrate formation simulations. When I load the trajectories in VMD and use “pbc wrap -compound res -all” to wrap the coordinates inside the box, still some of the methane molecules fall outside the box. I need to run the “pbc wrap -compound res -all” command again to bring those molecules inside the box. My simulations run with no error. Is it something I need to worry about? And why some molecules should still fall outside box?

This is a question for the vmd-l mailing list since this is not about a LAMMPS problem.

I see. Thanks Axel. I just wanted to make sure that this is not because of a bad simulation setup, etc.

How should anybody be able to tell, if your simulation setup is bad since you provide no information about it at all?