The Coarse Grained Molecular Dynamics of polybutadiene were conducted. The Coarse Grained Potential was estimated by using modeling function of J-OCTA. The method follows that in Reference (1). First, molecular dynamics was conducted for a single chain in vacuum (total time=10 [ns]) for cis-polybutadiene (N=50) based on Full Atomistic model.

Using the calculation results, the distributions of bond lengths, bond angles and dihedral angles between coarse grained units were evaluated, and coarse-grained potential was determined from the distributions obtained. About the non-bonded potential, interaction between coarse-grained units was evaluated directly.

The distributions of bond lengths, bond angles and dihedral angles between coarse grained units were showed in Fig. 1. The results of Full Atomistic model and the Coarse Grained model are in good agreement. Here, in Coarse Grained MD, calculation of bond dihedral angle potential was omitted due to calculation stability problems, but it is evident that the effect is small in this case.

NPT ensemble calculations were conducted at 300 [K], 0.1 [MPa] for each bulk state with different degrees of polymerization N. The total number of particles was the same at 5000 and long term simulation (400[ns]) was applied for the N=200 system.

The ratio of the mean square of radius of gyration (Rg) and end-to-end distance becomes to 6 as N increases (Fig. 2, left).

Finally, a bulk structure of Full Atomistic MD was created by using J-OCTA's reverse mapping function (Fig. 3). From the results of Coarse Grained MD, the monomers of the Full Atomistic model corresponding to each Coarse Grained unit were arranged and connected so that the direction of the each bond vector is matched. This process allows the creation of a more relaxed structure of Full Atomistic model.