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Over the past few decades, a large variety of nanocomposite polymer materials has attracted much attention due to their remarkable variability, which permits to tailor their structure to provide the desired physical property or functionality. In many cases, these materials offer significantly improved performance over conventional polymer materials, and thus are attractive for wide industrial applications. In this context, the development of a material design procedure is needed. There is a pressing need to incorporate an appropriate predictive approach in the realistic design. The report presents our progress of development of the simulation package MULTICOMP. This package provides a high-level set of integrated, versatile, GUI-based tools to design, simulate and analyze polymer nanocomposites composed of crosslinked/linear/branched copolymers containing different types of discrete fillers. This software can be used by people from different areas such as academic researchers and industrial developers. The package combine various ground-breaking modeling methodologies useful for studying of the formation and properties prediction of nanocomposites with interpenetrating polymer networks and hydrogels as well as microphase-separated organic–inorganic hybrid composite materials. The MULTICOMP simulation package can operate on currently available multi-teraflop/petaflop computational resources. This provide ability i) to design and study of the filled polymer systems containing up to several millions of atoms using fully atomistic molecular dynamics, ii) to simulate of coarse-grained nanocomposite models on length scales up to 10 μm and for time scales up to 100 μs. As a result, users can simulate, verify and analyze the performance of different polymer nanocomposites to evaluate the effect of different parameters on material properties, thereby improving processing recipes. As an example of using MULTICOMP package, we present our results on simulation of the effect of silica nanoparticles on the thermal and mechanical properties of thermoplastic silicone-urethane nanocomposite.