Required programs

The following programs are required for this tutorial:

• NAMD: Available at http://www.ks.uiuc.edu/Research/namd/ (for all platforms). Note that versions prior to NAMD 2.6 do not support the CMAP correction of the CHARMM forcefield.

• VMD: Available at http://www.ks.uiuc.edu/Research/vmd/ (for all platforms)

• Text Editor: We will use WordPad to view and edit some of the text files associated with the NAMD simulations. You may prefer to use Notepad or another text editor of your choosing. Microsoft Word is a word processing program and should not be used as a text editor.

• Plotting Program: We will use Microsoft Excel, available at
  http://office.microsoft.com/en-us/FX010858001033.aspx, to view and analyze output data from NAMD simulations. VMD also has an internal plotting program which we will use to examine output directly from NAMD log files. Other graphing programs which you may find useful are Mathematica, http://www.wolfram.com/, Matlab, http://www.mathworks.com/, and scilab, available at http://www.scilab.org/. Note that each of these programs, with the exception of scilab, requires you to purchase software. Scilab is a free program with capabilities nearly identical to Matlab. If Excel or any of the proprietary programs are unavailable to you, we encourage you to use scilab.