[gmx-users] the box margin plot in VMD

[Chris Neale]

You can use Gaussian98 cube format: 
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
Make a file like this:

title1
title2
0 x-origin y-origin z-origin
1 x-width 0.0 0.0
1 0.0 y-width 0.0
1 0.0 0.0 z-width
1 0 0 0 0
0

For example, if you want a cube that has a corner at  (0,0,0) and has a 
length of 10A (remember that it is A not nm) in each direction you would 
use the following file:

title1
title2
0 0 0 0
1 10 0 0
1 0 10 0
1 0 0 10
1 0 0 0 0
0

If you name the file *.cube then VMD will automatically recognize that 
it is Gaussian98 cube format. If the cube doesn't appear right away then 
set the representation to isosurface. You may notice that I have set 
zero atoms and then entered coordinates for one atom. This was 
intentional. Without the (second last line) coordinates it won't display.