Insights
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Which Molecular Dynamics Software Should I Choose for My Molecular Simulation? SPONGE, GROMACS, AMBER, or LAMMPS?
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.
Yijie Xia -
RMSD Algorithm Derivation and Practical 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.
Sidereus Ferrocene -
About Insights
Insights is a place to share methods, experiences and reflections on molecular modeling. Contributions are welcome via GitHub.
Yijie Xia