Systems can be too small for DOMDEC, and the limitations are implied by this note in

domdec.doc:******************
NOTES:
******************
The sub-box sizes are limited by the cut-off and the number of
sub-boxes as follows:
BOXX = system box size in X direction
NX = number of sub-boxes in X direction
RCUT = non-bonded cut-off + radius of the largest group
BOXX/NX = sub-box size in X direction
Then, for NX >= 2, the sub-box size in X direction must satisfy:
BOXX/NX <= BOXX - 2*RCUT
If your system violates this restriction, you can try reducing NX to 1 or by
increasing NX.

The inequality above can be expressed graphically; I've attached a PNG file illustrating the minimum number of cores needed as a function of edge length, assuming RCUT = 20 (CUTNB 14. Å + max group radius 6 Å).

The error message observed for an edge length that is too small looks like:

Try using more MPI nodes or set NDIR manually:
x-direction must have (a) 1 node or (b) at least 5 nodes
***** LEVEL -5 WARNING FROM <domdec> *****
***** DOMDEC node number limitation violated
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5

BTW, it should say "cores" instead instead of "nodes"; see the NDIR description in

domdec.doc