The packing of SubPc derivatives with halogens at β-positions is difficult to predict. However, they form diverse packing patterns that cannot be obtained using simple close-packed arrangements. Alternately, circular-shaped SubPc derivatives would adopt either a trigonal or P212121 structure. This alone is an important guideline for material design, but ideally, we would like to perfectly predict whether it will form a polar or nonpolar structure, in other words, whether it will adopt trigonal or P212121. In our previous studies, the formation of polar or nonpolar assemblies of F-substituted SubPc derivatives could be predicted through MD simulations. Herein, we further investigated whether MD simulations could be applied to SubPc derivatives substituted with different halogens than F. However, predicting the molecular assembly pattern is difficult, since it requires simulating all the possible assembled patterns while comparing their energy levels. We narrowed down the structures to P212121 and trigonal, which made it feasible to accurately compare the energy of both structures. R3c and P212121 structural formation using (M)SubPc-3Cl(α) were compared through MD simulation (Figure ) to confirm whether the experimentally obtained crystal structure (P212121) was energetically more favorable than R3c that could not be obtained. For the assembly structures that were not actually obtained, molecular assemblies obtained from other molecules were used as the initial structures, followed by optimization. For example, the molecular assemblies of rSubPc-3Cl(α) were utilized as the initial structures for trigonal assemblies of (M)SubPc-3Cl(α).