Computational Biophysics Workshop - Bremen, Oct. 17-21, 2011
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.
- 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.
