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From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Mar 11 2015 - 12:44:41 CDT
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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
confused.
Thanks in advance,
Kevin
Sent from my iPhone
On 12 Mar, 2015, at 00:07, Josh Vermaas <vermaas2_at_illinois.edu
<javascript:_e(%7B%7D,'cvml','vermaas2_at_illinois.edu');>> 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,
Kevin
PhD Candidate
Department of Physics and Material Science
City University of Hong Kong
ukevi_at_gmx.hk <javascript:_e(%7B%7D,'cvml','ukevi_at_gmx.hk');>
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