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Generating initial configurations of polymer melts above the entanglement molecular weight is a challenge in molecular dynamics and Monte Carlo simulations. In this work, we adapt an algorithm mimicking a chemical polymerization to all-atom force fields. The principle of this algorithm is to start from a bath of monomers between which bonds are created and relaxed sequentially. Our implementation is parallel and efficient. The parallelization is that of a classical molecular dynamics code and enables the user to generate large systems, up to 7 × 106 atoms. The efficiency of the algorithm comes from the linear scaling between the simulation time and the chain length in the limit of very long chains. The implementation is able to produce long polymer chains, up to ∼2000 carbon atoms, with thermodynamic and local structural properties in good agreement with their experimental and numerical counterparts. Moreover, the chain conformations are close to being equilibrated right after the end of the polymerization process, corresponding to only a few hundred of picoseconds of simulation, despite a systematical drift from Gaussian-like behavior when the density of reactively available monomers decreases. Finally, the algorithm proposed in this work is versatile in nature because the bond creation can be easily modified to create copolymers, block copolymers, and mixtures of polymer melts with other material. [ABSTRACT FROM AUTHOR]

We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.