From: Josh Vermaas (
Date: Thu Jul 10 2014 - 09:58:17 CDT

The origin doesn't reference atomic coodinates. I believe it does it at
the origin of the viewing window (the origin according to openGL), which
is a few transformation matrices removed from atomic positions. You can
see this really clearly if you play around with the other locations in
the GUI (Display->Axes), as the other locations VERY clearly refer to
window positions, not atom positions.
-Josh Vermaas
On 7/9/14, 9:48 PM, Chetan Mahajan wrote:
> Dear All,
> I have a small question on origin of coordinates as visualized in VMD.
> If I supply gromacs output coordinate file (say .gro) to VMD, how does
> VMD determine what should be the origin and then place atoms accordingly?
> I am asking this, since for my system, using command "axes location
> origin" in vmd, shows origin of the coordinates to be at the center of
> the box, as visualized at
> However, my origin in input file to gromacs was one of the vertices of
> the box and indeed almost all of the coordinates in input file to VMD
> are positive. How is that possible, if VMD shows origin at the center?
> Thanks in advance.
> regards
> Chetan