``` $ 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.