This tutorial 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 assumes that you already have a working knowledge of VMD and that NAMD has been correctly installed on your computer. For installation instructions, please refer to the NAMD Users's Guide. For the accompanying VMD tutorial go to
http://www.ks.uiuc.edu/Training/SumSchool03/Tutorials/vmd.
The tutorial is subdivided in three sections. The first one covers the basic initial steps of a molecular dynamics simulation, i.e., minimization and equilibration of your system. The second section introduces typical simulation techniques and the analysis of equilibrium properties. The last section deals with Steered Molecular Dynamics and the analyis of unfolding pathways of proteins. Finally, brief descriptions of all files needed for the simulations are provided in the appendices.
For a detailed description of NAMD the reader is referred to the NAMD User's guide located at
http://www.ks.uiuc.edu/Research/namd/current/ug/
The examples in the tutorial will focus on the study of ubiquitin - a small protein with interesting properties. Throughout the text, some material will be presented in separate ``boxes". Some of these boxes include complementary information to the tutorial, such as information about the biological role of ubiquitin, and tips or shortcuts for using NAMD. These boxes are not required for understanding the tutorial and may be skipped if you are short on time.
Boxes with an exclamation sign are specially important and should not be skipped.
