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: In order to perform simulations with the CG model in this tutorial, NAMD should be correctly installed on your computer. For installation instructions, please refer to the NAMD Users' 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/

• Plotting Program: Under Unix/MacOSX, one can use program xmgrace, available at http://plasma-gate.weizmann.ac.il/Grace/ (Free download), or gnuplot, http://www.gnuplot.info/ (Free download). Under Windows, one can use Microsoft Excel, available at
  http://office.microsoft.com/en-us/FX010858001033.aspx (Purchase required), or scilab, available at http://www.scilab.org/ (Free download). Other useful graphing programs, with versions available for both Unix/MacOSX and Windows, are Mathematica, http://www.wolfram.com/ (Purchase required) and Matlab, http://www.mathworks.com/ (Purchase required).

Most of the exercises in the tutorial are performed using Shape-Based Coarse-Graining (SBCG) Tools in VMD. The Tools are implemented as a set of plugins available with their Graphical User Interfaces (GUIs) through VMD menu:

Extensions $\rightarrow$ Modeling $\rightarrow$ CG Builder

Figure: Main Graphical User Interface for the CG Builder Tools in VMD. Available are several tools for two CG models, one of which is the SBCG model addressed in this tutorial.