VMD-L Mailing List
From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Mar 11 2015 - 10:09:09 CDT
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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
ukevi_at_gmx.hk
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