Combining Cryo-Electron Microscopy & Biomolecular Simulations: Discoveries Through a Computer Microscope


    Below is a list of the tutorials used at the summer school. Please click here to see a page with the updated versions of these tutorials.

  • Using VMD
    An introduction to VMD and its capabilities

  • NAMD Tutorial
    An introduction to NAMD and its capabilities

  • Molecular Dynamics Flexible Fitting (MDFF)
    Describes how to flexibly fit atomic structures into density maps using the MDFF method. This method can be used to obtain atomic models of macromolecular complexes by combining X-ray structures and cry-electron microscopy maps.

  • A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD
    Discusses setting up the system and calculations needed for free energy calculations of alchemical transformations within NAMD