From: Axel Kohlmeyer (
Date: Thu Jul 10 2014 - 15:47:34 CDT

On Thu, Jul 10, 2014 at 2:33 PM, Chetan Mahajan <> wrote:
> Thanks, Josh. Small question: So I guess there should be a way for VMD to
> display the origin of atomic coordinates, it has determined?

just draw some objects with the VMD draw or graphics commands. those
are in the atom coordinate system.

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

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.