TCB Hands-on Workshop in Urbana


    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
  • Shape-Based Coarse Graining
    Reviews the use of the coarse graining beads to to represent overall shapes of proteins or lipid membranes.

  • User-Defined Forces in NAMD
    Guides users of VMD and NAMD in the use of the tclForces and tclBC scripts.
  • A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD
    Discusses setting up the system and calculations needed for free energy calculations of alchemical transformations within NAMD.
  • A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD
    Discusses setting up the system and calculations needed for adaptive biasing force calculations of conformational transitions within NAMD.
  • Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
    A tutorial that uses structural and sequence alignment to learn about the evolution of tRNA synthetases.

  • Evolution of Translation EF-Tu: tRNA
    Provides an advanced lesson in the MultiSeq bioinformatic analysis environment.
  • Evolution of Translation: The Ribosome
    Leads the reader through major features of the ribosome, the primary translation machinery of the cell.
  • Stretching Deca-Alanine Tutorial
    An introduction to IMD and SMD simulations with VMD and NAMD

  • Simulation of Water Permeation Through Nanotubes
    A tutorial simulating water diffusion and permeation through nanotubes

  • Aquaporins Tutorial
    A tutorial that uses Bioinformatics tools within VMD to find important structural features in aquaporins from evolutionary studies

  • Parameterization of a Novel Residue
    Tutorial on determining new force field parameters to describe novel system components of a new molecule
  • Membrane Proteins Tutorial
    Step by step tutorial for setting up and running molecular dynamics simulations of membrane proteins.