Appendix B: Sample Tutorials
VMD Molecular Graphics
This tutorial, available online at http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/, introduces new users to VMD and its capabilities. It can also be used as a refresher course for the occasional VMD user wishing to employ this program more productively.
The tutorial covers the basics of molecular graphics representations and will introduce everything you need to know to generate nice graphics. The tutorial also walks scientifically oriented users through the essentials of scripting in VMD, which provides powerful, easy-to-use tools that cannot be offered by a simple graphical user interface.
The examples in the tutorial focus on ubiquitin -- a small protein with interesting properties.
NAMD
This tutorial, available online at http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/, provides a first introduction to NAMD and its basic capabilities. It can also be used as a refresher course for the non-expert NAMD user.
The tutorial covers the initial steps of a molecular dynamics simulation, that is, minimization and equilibration of the system. The tutorial then goes on to introduce typical simulation techniques and the analysis of equilibrium properties. Finally, the tutorial deals with steered molecular dynamics and the analysis of unfolding pathways of proteins.
The examples in the tutorial focus on ubiquitin -- a small protein with interesting properties.
For more information on the workshop tutorials, please visit: http://www.ks.uiuc.edu/Training/TutorialsOverview/index.html