[gmx-users] rhombic dodecahedron construction

Tsjerk Wassenaar tsjerkw at gmail.com
Fri May 23 10:16:24 CEST 2014

Hi Trayder,

You can check the code of insane (
http://cgmartini.nl/cgmartini/index.php/insane), which sets up such a
rhombic dodecahedron when -pbc optimal is given. Essentially, the routine
boils down to:

1. Determining the diameter of the protein in the XY directions
2. Set the first vector u=(diam+pbcdistance, 0, 0)
3. Set the second vector v=(u/2, cos30*u, 0)
4. Set the third vector to w=(u/2, cos30*u/3, Z), where

Changing the Z-dimension of the box (or the whole box) can be done manually
(or using awk), changing the numbers of the last line in the gro file,
which corresponds to (ux vy wz uy uz vx vz wx wy). Finally, note that the
box (any box) is written in its triclinic representation, which is easiest
to handle mathematically.

Hope it helps,


On Fri, May 23, 2014 at 4:42 AM, Trayder Thomas
<trayder.thomas at monash.edu>wrote:

> Hi,
> I'm trying to figure out how to construct a rhombic dodecahedron for a
> membrane system.
> The manual (Section 3.2.1) states:
> "There are two different orientations of a rhombic dodecahedron that
> satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the
> orientation which has a square intersection with the xy-plane. This
> orientation was chosen because the first two box vectors coincide with the
> x and y-axis, which is easier to comprehend. The other orientation can be
> useful for simulations of membrane proteins. In this case the cross-section
> with the xy-plane is a hexagon, which has an area which is 14% smaller than
> the area of a square with the same image distance. The height of the box
> (cz) should be changed to obtain an optimal spacing."
> I can't figure out how to construct the system with a hexagon on the x-y
> plane, I presume I can rotate the box but I can only visualise the result
> as a triclinic cell.
> I also can't figure out how to adjust the height of the box, editconf only
> accepts a single magnitude for dodecahedron vector lengths.
> Any help would be greatly appreciated.
> Thanks in advance,
> -Trayder
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Tsjerk A. Wassenaar, Ph.D.

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