editconf -d ignores system diameter
$ gmx solvate -box 1 -o water.gro
$ gmx editconf -f water.gro -o water2.gro -d 0.001 -noc
$ diff water.gro water2.gro
93c93
< 1.00000 1.00000 1.00000
---
> 0.00200 0.00200 0.00200
https://manual.gromacs.org/current/onlinehelp/gmx-editconf.html
According to the documentation for editconf,
With -d and cubic, dodecahedron or octahedron boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance.
the box vectors should be 1.000 + 2*0.001 = 1.002
editconf appears to be ignoring the system and setting the first term to zero.