# Control over dodecahedron box

**URL:** <https://gromacs.bioexcel.eu/t/control-over-dodecahedron-box/9721>\
**Category:** User discussions\
**Created:** [July 23, 2024, 7:17pm UTC](https://gromacs.bioexcel.eu/t/control-over-dodecahedron-box/9721 "2024-07-23T19:17:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![com\_gro](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\
**Post date:** [July 23, 2024, 7:17pm UTC](https://gromacs.bioexcel.eu/t/control-over-dodecahedron-box/9721/1 "2024-07-23T19:17:51Z")

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Hello,

I am using the following commands to create a dodecahedron box. I want a dodecahedron box with a long y-axis. However, when I use box sizes such as 20 45 20 or 20 60 20, I end up with the same number of atoms, which means the box size does not change. How can I control the dodecahedron box size? I need a box with a long y-axis for pulling a protein along this axis, while x and z axes of 20 nm are acceptable. Additionally, I want to keep my protein at the top edge of the y-axis. I’ve tried using a cubic box, which works, but I want to experiment with a dodecahedron box to reduce the system size.

Here is the command I used:

```auto
gmx editconf -f clpb_traj1_50_rotated.gro -o _custom_box_.gro -c -box 20 45 20 -bt dodecahedron

```

**Output of above command:**  
Note that major changes are planned in future for editconf, to improve usability and utility.  
Read 36805 atoms  
Volume: 8734.14 nm^3, corresponds to roughly 3930300 electrons  
No velocities found  
system size : 13.057 15.374 13.608 (nm)  
diameter : 16.489 (nm)  
center :-13.372 3.091 18.381 (nm)  
box vectors : 14.851 14.851 39.602 (nm)  
box angles : 90.00 90.00 90.00 (degrees)  
box volume :8734.14 (nm^3)  
shift : 28.372 11.909-11.310 (nm)  
new center : 15.000 15.000 7.071 (nm)  
new box vectors : 20.000 20.000 20.000 (nm)  
new box angles : 60.00 60.00 90.00 (degrees)  
new box volume :5656.85 (nm^3)

 ![box](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c2d1df4317522d7f31143a7b6a7e2d0c3ab23769.jpeg)

Thanks

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<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [August 12, 2024, 8:49am UTC](https://gromacs.bioexcel.eu/t/control-over-dodecahedron-box/9721/2 "2024-08-12T08:49:34Z")

</div>

Your `gmx editconf` command only changes the box dimensions, it does not remove (or add atoms). I would be careful changing (especially reducing) the box size of a system with solvent. When increasing the box size you can fill the void with new solvent and re-equilibrate the system. It’s difficult to avoid collisions, due to periodic overlap, when reducing the box size of a “full” box.