The ubiquity of planets and diversity of planetary systems reveal planet formation encompass many complex and competing processes. In this series of papers, we develop and upgrade a population synthesis model as a tool to identify the dominant physical effects and to calibrate the range of physical conditions. Recent planet searches leads to the discovery of many multiple-planet systems. Any theoretical models of their origins must take into account dynamical interaction between emerging protoplanets. Here, we introduce a prescription to approximate the close encounters between multiple planets. We apply this method to simulate the growth, migration, and dynamical interaction of planetary systems. Our models show that in relatively massive disks, several gas giants and rocky/icy planets emerge, migrate, and undergo dynamical instability. Secular perturbation between planets leads to orbital crossings, eccentricity excitation, and planetary ejection. In disks with modest masses, two or less gas giants form with multiple super-Earths. Orbital stability in these systems is generally maintained and they retain the kinematic structure after gas in their natal disks is depleted. These results reproduce the observed planetary mass-eccentricity and semimajor axis-eccentricity correlations. They also suggest that emerging gas giants can scatter residual cores to the outer disk regions. Subsequent in situ gas accretion onto these cores can lead to the formation of distant (> 30AU) gas giants with nearly circular orbits.
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