Contents

• Overview of MDFF commands
• A simple MDFF example
  • Generating a simulated density map
  • Converting the density map to an MDFF potential
  • Rigid-body docking the structure into the density map
  • Preparing the initial structure
  • Defining secondary structure restraints
  • Running the MDFF simulation with NAMD
  • Visualizing the MDFF trajectory
  • Calculating the root mean square deviation
  • Calculating the cross-correlation coefficient
  
  
• MDFF with explicit solvent
  • Preparing the initial structure
  • Preparing the density map
  • Running the MDFF simulation
  • Analyzing the results
  
  
• MDFF with Domain Restraints
  • Preparing the initial structure
  • Setting up the Domain PDB file
  • Running the MDFF simulation
  • Analyzing the results
  
  
• MDFF with Symmetry Restraints
  • Preparing the initial structure
  • Setting up the Symmetry PDB file
  • Setting up the Transformation Matrix File
  • Running the MDFF simulation
  • Analyzing the results
  
  
• xMDFF: MDFF for Low-Resolution X-ray Crystallography
  • Preparing the initial structure
  • Setting Up NAMD Configuration Files for xMDFF
  • Analysis of xMDFF refinements
  
  
• MDFF GUI and Timeline Analysis
  • Setting up simulations with the MDFF GUI
  • Interactive MDFF
  • Timeline Analysis