Free Energy Surfaces

Free Energy Surfaces

• Basic umbrella sampling in sander
  • Learning objectives
  • Relevant literature
  • Activities
    • Modifying the mdin file
    • Defining restraints in the disang file
    • Preparing the files needed for a 1-dimensional umbrella sampling
• QM/MM Umbrella sampling using path collective variables
  • Learning objectives
  • Relevant literature
  • Activities
  • Introduction
  • Use colvars restraints within Sander
  • Convert Amber NMR Restraint DISANG file to colvars CONFIG format
  • Convert ndfes Metafile to a colvars CONFIG format that biases the the surface using Path Collective Variables
  • Run QM/MM PathCV umbrella sampling using colvars implementation within Sander
  • Analyze the PathCV umbrella sampling using ndfes
• Applying RMSD restraints in Sander using the Colvars library
  • Learning objectives
  • Relevant literature
  • Activities
  • Introduction
  • Use colvars restraints within Sander
  • Defining the RMSD restraint within the colvars CONFIG file