BioSimSpace

Author: Rory Portman

RNA_AFE: Molecular Dynamics Simulations Setup and Analysis for Small Molecule-RNA Complexes

Introduction

The notebooks included on this page cover the necessary steps to setup, run and analyse Molecular Dynamics Simulations for Small Molecule-RNA complexes:

• Loading, parameterising, solvating and combining the Ligands, the RNA and the Waters.
• Running Equilibration and Minimisation for the Small Molecule:RNA system.
• Writing scripts to initiate 100 ns molecular dynamics simulations using various simulation engines.
• Analysing MD simulations and producing plots for reports.