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

  • Topology File Tutorial
    Guides users in how to create topology and parameter information needed for molecular dynamics simulations when it otherwise doesn't exist, by using existing topology information for other molecules without the need for new parameter development

  • 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.