Getting Started

• If you are performing this tutorial at a Computational Biophysics Workshop offered by the Theoretical and Computational Biophysics Group, a copy of the files needed for this tutorial have been set up for you. The files exist in the directory called Workshop in your home directory. In a Terminal window type:

  cd ~/Workshop/namd-tutorial/namd-tutorial-files

  This will place you in the directory containing all the necessary files.

• If you have downloaded this tutorial at home, you will also need to download the appropriate files, unzip them, and place them in a directory of your choosing. You should then navigate to that directory in a similar manner as described directly above. The files for this tutorial are available at http://www.ks.uiuc.edu/Training/Tutorials/.

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