VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jul 10 2014 - 12:25:04 CDT

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:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html). 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 <vermaas2_at_illinois.edu
> <mailto: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
>
>