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

User discussions
1

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).

2

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.

3

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