This contains input decks and analysis scripts for simulating the SMOG-ion class of structure-based models with ions. For more information about the models, consult the original references and https://smog-server.org.
The directory "InputDecks" contains the files needed to run simulations of RNA molecules with explicit ions, including the force field files, settings files and Python scripts.
The directory "Analysis" contains analysis tools that have been used in publications.
The directories refer to the following studies:
Wanes_biorxiv_2025: G Wanes, U Mohanty, P C Whitford. Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.