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We have developed all-atom structure-based model (SMOG) generalization of Manning counterion condensation theory to RNA and riboswitches that is explicit divalent (magnesium) but implicit monovalent ion. The C++ codes and files are available online
All-atom stucture-based models, SMOG v2.4, and OpenSMOG (v 1.1.0) are both open souce and freely available at https:/smog-server.org/smog2. The OpenSMOG is a python library for molecular dynamics (MD) simulations of structure-based models that can be installed via pip or conda.