Getting Started

In order to begin the tutorial, you should open an MS-DOS command window by clicking Start $\rightarrow$ Programs $\rightarrow$ Accessories $\rightarrow$ Command Prompt. This is the window that you will type commands into during the tutorial. This window will be referred to as a ``Terminal'' window. You can create another one of these windows if needed by following the same process.

In order to run the tutorial, you will need the appropriate files. The files for this tutorial are available at http://www.ks.uiuc.edu/Training/Tutorials/. You should download the files and unzip them in a convenient location. You should then use the Terminal window to navigate to the directory containing these files. For instance, if the files were unzipped in your home directory, you would type:

$>$ cd C:\Documents and Settings\<account-name>\Workshop\
namd-tutorial\namd-tutorial-files

This will place you in the directory containing the tutorial files.

Figure 1: Directory Structure for tutorial exercises. Output for all simulations is provided in an ``example-output'' subdirectory within each folder shown.