# Editconf -bt dodecahedron -c does not appear to place protein in middle of dodecahedron

**URL:** <https://gromacs.bioexcel.eu/t/editconf-bt-dodecahedron-c-does-not-appear-to-place-protein-in-middle-of-dodecahedron/11380>\
**Category:** User discussions\
**Created:** [January 27, 2025, 11:00am UTC](https://gromacs.bioexcel.eu/t/editconf-bt-dodecahedron-c-does-not-appear-to-place-protein-in-middle-of-dodecahedron/11380 "2025-01-27T11:00:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ackbar03](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@ackbar03](https://gromacs.bioexcel.eu/u/ackbar03)\
**Post date:** [January 27, 2025, 11:00am UTC](https://gromacs.bioexcel.eu/t/editconf-bt-dodecahedron-c-does-not-appear-to-place-protein-in-middle-of-dodecahedron/11380/1 "2025-01-27T11:00:32Z")

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GROMACS version: 2023.3-plumed\_2.10.0\_dev  
GROMACS modification: Yes (with plumed)

Hi,

I am a bit confused over the behavior of editconf and solvate.

I used editconf to center my protein in a dodecaheron with options  
-bt dodecahedron -c -d 1.0

And then solvated the system with solvate.

When I examine the system in pymol after solvation, the water appears to be added to a cube rather than a dodecaheron and the protein does not appear to be in the center of the cube either, but a the top right hand corner when viewed from the XY plane. It is only centered in the Z plane.

Is this expected behavior? It is a bit confusing as it appears to me that there is a lot of unnecessary empty space, and my protein keeps floating out of the cube (which I know can be corrected later on with trajconv).

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**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [January 27, 2025, 11:15am UTC](https://gromacs.bioexcel.eu/t/editconf-bt-dodecahedron-c-does-not-appear-to-place-protein-in-middle-of-dodecahedron/11380/2 "2025-01-27T11:15:21Z")

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This is just a visualization problem, it is not really the shape of the box. Try to re-wrap your coordinates with `trjconv` and the flag `-ur compact`, you should be able to recover the “real” shape of the box.

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**Author:** ![ackbar03](https://avatars.discourse-cdn.com/v4/letter/a/f0a364/32.png) [@ackbar03](https://gromacs.bioexcel.eu/u/ackbar03)\
**Post date:** [January 27, 2025, 12:44pm UTC](https://gromacs.bioexcel.eu/t/editconf-bt-dodecahedron-c-does-not-appear-to-place-protein-in-middle-of-dodecahedron/11380/3 "2025-01-27T12:44:51Z")

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I see, I played around with it and it makes more sense now. Thanks a lot for the prompt reply.