The self-assembling behavior of conjugated regioregular poly(3'-alkylthiophene) (P3AT) polymers with various grafting density and length of alkyl side-chains are systematically examined by the coarse-grained molecular dynamics (CGMD) simulations. The effective CG interaction potentials are determined by taking into account the atomistic structural details from all-atom (AA) MD through the mapping route between the AAMD and CGMD data via the Iterative Boltzmann Inversion (IBI) methods. Except the non-bonded interaction potential between two thiophenes is modified by simply calculating the potential energy curve for them in a trans-orientation. With the dihedral angle constraint, two types of the grafted side-chains, which are located on both sides (anti-) and the same side (syn-) of the backbones, are modeled at GD = 100%, 33% and 50%, 25%, respectively. For densely grafted side-chains, such as when GD = 100% and 50%, the strong pep attraction between the thiophene rings plays the most dominant role on the self-assembling behavior of P3AT molecules. Thus, we observe the formation of single-walled and double-walled lamellae, which however become more twisted with increasing the length of side-chains at GD = 100% and 50%, respectively. This is not surprising as longer flexible alkyl side-chains cause the backbone thiophene rings to suffer a larger distortion degree. When the grafting density is reduced significantly, not only the pep attraction between the thiophene rings can induce the ordered packing of main-chains, but also the significant space between the side-chains can facilitate the interdigitation and aggregation of side-chains. Accordingly, for the poly(3'-nonylthiophene), poly(3'-dodecylthiophene), and poly(3'-pentadecylthiophene) molecules with 25% grafting density, we predict the formation of polygonal columns, which are formed by the packing of main-chains parallel to the column axes and the aggregation of the side-chains within the columns. When the side-chain length is increased further, these aggregated long side-chains can no longer be constrained within the polygonal minor-domains. Instead, double-walled lamellae become the most stable phase for P3AT molecules with 25% GD. (C) 2015 Elsevier Ltd. All rights reserved.