Protocol for calculating binding free energy of RNA:RNA interactions through molecular dynamics simulations using adaptive biasing force technique.

The adaptive biasing force (ABF) technique allows sampling to proceed in a flat free energy surface when performing molecular dynamics (MD) simulations. Here, we present a protocol to perform MD simulations using the ABF technique and apply it to calculate the binding free energy of an RNA:RNA interaction. We describe steps for server setup, test running software, and building molecular models. We then detail procedures for running and configuring ABF-MD simulations and analyzing binding free energy and structural change. For complete details on the use and execution of this protocol, please refer to Fujita et al. and Kameda et al..