1.
STAR Protoc
; 5(3): 103223, 2024 Jul 30.
Artículo
en Inglés
| MEDLINE
| ID: mdl-39083381
RESUMEN
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.1 and Kameda et al.2.