From: Chetan Mahajan (
Date: Thu Jul 10 2014 - 13:33:08 CDT

Thanks, Josh. Small question: So I guess there should be a way for VMD to
display the origin of atomic coordinates, it has determined?

On Thu, Jul 10, 2014 at 12:25 PM, Josh Vermaas <>

> Transformation matrices. To go from "world" (atomic) coordinates to what
> is on the screen, there are a few transformation matrices that get applied
> (look at the molinfo command:
> The
> center_matrix, rotate_matrix, and scale_matrix are applied to the atomic
> coordinates and that's what shows up on the screen. The default behavior is
> to set these matricies such that the whole extent of the displayed
> atomselection of the top molecule is in the middle of the screen. The
> extension of the files in question are irrelevant. gro, pdb, dcd, trr, etc,
> all get treated the same way.
> -Josh Vermaas
> On 7/10/14, 1:18 PM, Chetan Mahajan wrote:
> 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 <>
> 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
>> 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