Computational Biophysics Workshop - Pittsburgh, May 10-14, 2010
TCB Hands-on Workshop in Urbana
Tutorials
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.