From: Kevin C Chan (
Date: Wed Mar 11 2015 - 10:09:09 CDT

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