VMD-L Mailing List

From: Chetan Mahajan (chetanvm10_at_gmail.com)
Date: Wed Jul 09 2014 - 20:48:53 CDT

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 https://www.dropbox.com/s/zty7hlofjxbez93/snapshot-vmd.pdf
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