# [gmx-users] rhombic dodecahedron construction

Trayder Thomas trayder.thomas at monash.edu
Mon May 26 07:19:47 CEST 2014

```Thanks Tsjerk,

That works great, and thanks for the vectors I can see where I went wrong
calculating them myself.

Thanks again,
-Trayder

On Fri, May 23, 2014 at 6:16 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> Z=(protZlength+pbcdistance)
>
> 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,
>
> Tsjerk
>
>
>
> 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.
> >
> > -Trayder
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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```