Introduction

This tutorial introduces new users to VMD and its capabilities. It can also be used as a refresher course for the occasional VMD user wishing to employ this program more productively. This tutorial has been designed specifically for VMD 1.8.5 or later versions, and should take about 3 hours to complete in its entirety.

The tutorial is subdivided into three separate units of increasing complexity. The first unit covers the basics of molecular graphics representations and will introduce everything you need to know to generate nice graphics. The other two units are targeted toward the scientifically-oriented user and focus on scripting in VMD. While scripting may be skipped by the non-technical users, we encourage everyone to give it a try as it provides some very powerful (and easy to use) tools that cannot be offered by a simple graphical user interface.

The examples in the tutorial will focus on the study of ubiquitin - a small protein with interesting properties. Throughout the text, some material will be presented in separate ``boxes". These boxes include complementary information to the tutorial, such as information about the biological role of ubiquitin, and tips or shortcuts for using VMD.

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/ (for all platforms)

• Plotting Program: You will need a program to view a graph output from VMD. VMD has an internal plotting program, or you can use an external application. Which program you can use will depend on your operating system. Some examples include
  • Unix/Linux: xmgrace, http://plasma-gate.weizmann.ac.il/Grace/

  • Windows: Excel, http://office.microsoft.com/en-us/FX010858001033.aspx (Purchase required)

  • Mac/Multiple Platforms: Mathematica, http://www.wolfram.com/ (Purchase required); gnuplot, http://www.gnuplot.info/(Free download)

Getting Started

You can find the files for this tutorial in the vmd-tutorial-files directory. Below you can see in Fig. 1 the files and directories of vmd-tutorial-files.

Figure 1: Directory structure of vmd-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.