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: Nedit is a text editor which will be used throughout this tutorial to view and edit some of the files associated with the simulations. There are others such as pico, emacs, jot, and vi. Feel free to use whichever text editor you are most comfortable with.

• Plotting Program: We will use the free program xmgrace, available at http://plasma-gate.weizmann.ac.il/Grace/, to view and analyze output data from NAMD simulations. VMD also has an internal plotting program which may be used to examine output directly from NAMD log files. Other useful graphing programs are Mathematica, http://www.wolfram.com/ (Purchase required), Matlab, http://www.mathworks.com/ (Purchase required), and gnuplot, http://www.gnuplot.info/ (Free download).