Introduction

This tutorial is designed to guide users of VMD and NAMD in the use of tclForces and tclBC. It is assumed that you already have a working knowledge of VMD and NAMD, as well as the Tcl language. For the accompanying VMD and NAMD tutorials go to:
http://www.ks.uiuc.edu/Training/Tutorials/
This tutorial has been designed specifically for VMD 1.8.5, and should take about 5 hours to complete in its entirety.

The tutorial is subdivided into two separate units, one for tclForces and one for tclBC. These script-based facilities make possible virtually any perturbation of your system, and after completing this tutorial you will have the basic skills to use them.

Throughout the text, some material will be presented in separate ``boxes". These boxes include complementary information to the tutorial and tips or technical details that can be further explored by the advanced user.

Tcl code is written in this font. When a line ends with a backslash ($\backslash$) this means that there should be no line break ...don't press enter, just keep typing!

If you have any questions or comments on this tutorial, please email the TCB Tutorial mailing list at tutorial-l@ks.uiuc.edu. The mailing list is archived at http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/tutorial-l/.

Required programs

The following programs are required for this tutorial:

• VMD: Available at http://www.ks.uiuc.edu/Research/vmd

• NAMD: Available at http://www.ks.uiuc.edu/Research/namd

Getting Started

You can find the files for this tutorial in the forces-tutorial-files directory. Fig. 1 shows the files and directories of forces-tutorial-files.

Figure 1: Directory structure of forces-tutorial-files

To start VMD type vmd in a Unix terminal window, double-click on the VMD application icon in the Applications folder in Mac OS X, or click on the Start $\rightarrow$ Programs $\rightarrow$ VMD menu item in Windows.