VMD-L Mailing List

From: Chetan Mahajan (chetanvm10_at_gmail.com)
Date: Thu Jul 10 2014 - 12:18:34 CDT

Thanks, Josh. How does VMD visualize atoms placed at coordinates mentioned
in input file (e.g. .gro file) without deciding what should be the origin?
Does the extension, .gro, suggest to VMD that origin of coordinates should
be at one of the vertices of the box?
Thanks
Chetan

On Thu, Jul 10, 2014 at 9:58 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
> 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
>
>
>