From: ruiyan (
Date: Fri Jun 16 2017 - 12:21:42 CDT

Dear Axel,

Thanks for your explanation and suggestion. When I use pbc box -center bb, all atoms are inside the box.

Best wishes,


发件人: "Axel Kohlmeyer" <>
发送时间: 2017-06-17 00:20:00 (星期六)
收件人: ruiyan <>
抄送: "Vmd l" <>
主题: Re: vmd-l: problem of displaying simulation box

On Fri, Jun 16, 2017 at 11:04 AM, ruiyan <> wrote:
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.

​this happens, because VMD does not read the box origin, only the length.
when you display the box with pbc box, you have to specify the coordinates of the center of the box with the -center flag. the default setting may not be consistent with your geometry




Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.