From: Josh Vermaas (
Date: Wed Mar 11 2015 - 11:07:36 CDT

Hi Kevin,

Does "pbc get" give you what you expect? I suspect what is happening is
that it is drawing a box of the correct size, but at the wrong origin. I
don't typically draw the boxes, so someone else may have more info, but
I suspect if you recentered the trajectory so that it is centered on the
origin, the box will encompass your trajectory.

-Josh Vermaas

On 03/11/2015 10:09 AM, Kevin C Chan wrote:
> Dear Users,
> I am currently confused by the pbc plugin shipped with VMD 1.9.2. I
> have executed the following steps:
> mol new ionized.psf
> mol addfile npt-1.dcd
> pbc readxst npt-1.xst
> pbc box
> However, on the OpenGL display, it gives a box besides my system. I
> have checked my PBC parameters by drawing a sphere at the box centre
> manually read from the xst file and it is lying at the centre of my
> system. I have no idea what could be possibly wrong to cause a box
> appearing at another unexpected position (few nm away).
> Thanks in advance,
> Kevin
> PhD Candidate
> Department of Physics and Material Science
> City University of Hong Kong
> <>