From: ruiyan (
Date: Fri Jun 16 2017 - 10:04:30 CDT

Dear all,

I want to show trajectory from Lammps dump file. I created a Al crystal (FCC) in lammps with a size of (0 11 0 11 0 11) and defined the box with a size of (0.25 10.25 0.25 10.25 0.25 10.25). In this way, all atoms should be inside the box. I checked the dump file and all atoms are indeed inside the box. However, when I display the system in VMD and show the simulation box using pbc box command, I found that some atoms are on the boundary of the box. Why this happens? What command should I use to let all atoms locate inside the box? Thanks.