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The developed protocol first relaxes soft polymer chains in a stage analogous to thermal activation, which promotes crystallinity, and subsequently incorporates chain stiffening to reproduce crystal growth during cooling. The approach is validated against experimental SAXS measurements by computing intensity profiles from the electronic density of simulated Nafion. The results highlight the strong influence of side chain distribution on crystallinity, emphasizing its role in the formation of realistic semi-crystalline morphologies. Key processes, including chain ordering, local alignment, and molecular packing, are resolved, providing an improved understanding of structure\u2013property relationships. 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