Required Programs

The following programs are required for this tutorial:

• VMD: The tutorial assumes that you already have a working knowledge of VMD, which is available at http://www.ks.uiuc.edu/Research/vmd/ (for all platforms)
  • The VMD tutorial is available at
    http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/
• NAMD: The latter sections assume that NAMD has been correctly installed on your computer. However, NAMD is not needed to complete this tutorial, but it is recommended. For installation instructions, please refer to the NAMD Users's Guide.
  • The NAMD tutorial is available in both Unix/MacOSX and Windows versions:
    http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/
    http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/

• a text editor of your choice (we offer a few easy-to-use recommendations):
  • UNIX: nedit (www.nedit.org)
  • Windows XP: WordPad (included with OS). We recommend using WordPad as opposed to NotePad for this tutorial. However, please ensure that you save any files in this tutorial as .txt files, as opposed to .rtf or .doc files.
  • Mac OS X: Smultron (smultron.sourceforge.net), TextEdit (included with OS)

• a command prompt, such as a terminal in UNIX, Terminal.app in Mac OS X, or the DOS command prompt in Windows.