From: Kevin C Chan (
Date: Wed Mar 11 2015 - 12:44:41 CDT

Thanks for the reply.

Yes indeed "pbc get" gives the correct box size but I'm wondering why I
have to recenter my trajectory as I don't think there is a shift of origin
of the system (or the unit cell) according to the xst file. But "pbc box
-center unitcell" did draw the box at an unknown position. That's why I'm

Thanks in advance,

Sent from my iPhone

On 12 Mar, 2015, at 00:07, Josh Vermaas <
<javascript:_e(%7B%7D,'cvml','');>> wrote:

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,

PhD Candidate
Department of Physics and Material Science
City University of Hong Kong <javascript:_e(%7B%7D,'cvml','');>