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This study aims to provide preliminary findings on the integration of reactive molecular dynamics (RMD) simulations with evidence-based instructional strategies to enhance STEM identity and motivation in first-year, first-generation, and low-income college students. Six students from two Hispanic-serving institutions in central California participated in a three-week winter research program, which included 10 instructional modules on materials science topics. The program incorporated hands-on RMD simulation training to deepen students’ understanding of chemical reactions at the atomic level. Data collected through pre- and post-surveys and open-ended responses revealed increased STEM identity and motivation, along with improved interest, competence, performance, and recognition in STEM. Additionally, the program demonstrated the potential to enhance students’ persistence in STEM learning through positive experiences such as hands-on activities, peer collaboration, and simulations. These findings suggest the winter research program highlighting RMD may strengthen STEM identity and motivation in materials science education.