Notes on SPONGE molecular simulation methods, experiences and reflections.https://spongemm.cn/enhttps://spongemm.cn/en/insights/how-to-choose-molecular-dynamics-software/https://spongemm.cn/en/insights/how-to-choose-molecular-dynamics-software/Facing molecular dynamics simulation software such as SPONGE, GROMACS, AMBER, LAMMPS, GPUMD, NAMD, CHARMM, Material Studio, Desmond, and OpenMM, how should beginners choose? This article discusses how to choose suitable software for a specific molecular simulation project from the perspectives of licensing, inherited workflows, systems and force fields, advanced method support, community and usability, hardware platforms, and extensibility.Tue, 19 May 2026 00:00:00 GMTYijie Xiahttps://spongemm.cn/en/insights/rmsd-algorithm-derivation-and-applications/https://spongemm.cn/en/insights/rmsd-algorithm-derivation-and-applications/When choosing different levels of theory for structure-related calculations on different systems, RMSD and the Kabsch algorithm can be used to evaluate structural similarity between methods.Mon, 11 May 2026 00:00:00 GMTSidereus Ferrocenehttps://spongemm.cn/en/insights/about-insights/https://spongemm.cn/en/insights/about-insights/Insights is a place to share methods, experiences and reflections on molecular modeling. Contributions are welcome via GitHub.Tue, 05 May 2026 00:00:00 GMTYijie Xia