For such physics issues of a specific case, you can follow what you have found in the literature. This is just a comment from scientific point of view. In addition, the spin configuration of edges chosen in the study of transport properties of zigzag GNR also depends on the desired topics under study. If you study the spin-dependent transport properties, the AFM configuration of edges of zigzag GNR must be necessary. For armchair GNR or bilayer GNR, you had better first check their magnetic ground states. Since these system were well studied in literature, you can check some of previous theoretical work.
