• Program

• Instructors

• Lectures

• Tutorials

• Participants

• Photo Gallery

• Evaluation

• NRBSC Site

• Home

Computational Biophysics Workshop - Pittsburgh, May 16-20, 2011

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.