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

  • VMD Molecular Graphics Tutorial
    An introduction to VMD and its capabilities.

  • NAMD Molecular Dynamics/Steered Molecular Dynamics Tutorial
    An introduction to NAMD and its capabilities.

  • Evolution of Protein: Aspartyl-tRNA Synthetase
    A tutorial that uses structural and sequence alignment to learn about the evolution of tRNA synthetases.

  • Topology File Tutorial
    An introduction on how to generate parameter information for a molecule based on topology information from other molecules.

  • Simuation of Water Permeation Through Nanotubes Tutorial
    A tutorial simulating water diffusion and permeation through nanotubes.

  • Stretching Deca-Alanine Tutorial
    An introduction to IMD and SMD simulations with VMD and NAMD.

  • Parameterization of a Novel Residue
    Takes participants through a comprehensive example of how one investigates, sets up, and simulates a small nonstandard ligand bound to a protein system; specifically, the glutaminase subunit of the hisH-hisF system and determining the parameters for the non-standard residue.