Introduction

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It is developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. Among molecular graphics programs, VMD is unique in its ability to efficiently operate on multi-gigabyte molecular dynamics trajectories, its interoperability with a large number of molecular dynamics simulation packages, and its integration of structure and sequence information.

Figure 1: Example VMD renderings.

Key features of VMD include:

• General 3-D molecular visualization with extensive drawing and coloring methods
• Extensive atom selection syntax for choosing subsets of atoms for display
• Visualization of dynamic molecular data
• Visualization of volumetric data
• Supports all major molecular data file formats
• No limits on the number of molecules or trajectory frames, except available memory
• Molecular analysis commands
• Rendering high-resolution, publication-quality molecule images
• Movie making capability
• Building and preparing systems for molecular dynamics simulations
• Interactive molecular dynamics simulations
• Extensions to the Tcl/Python scripting languages
• Extensible source code written in C and C++

This article will serve as an introductory VMD tutorial. It is impossible to cover all of VMD's capabilities, but here we will present several step-by-step examples of VMD's basic features. Topics covered in this tutorial include visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animate and analyze the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.

Downloading VMD

Before staring the tutorial you need to download the current version of VMD. This tutorial requires VMD version 1.9 or later. VMD supports all major computer platforms and can be obtained from the VMD development homepage
http://www.ks.uiuc.edu/Research/vmd. Follow the instruction online to install VMD in your computer. Once VMD is installed, to start VMD:

• Mac OS X: Double click on the VMD application icon in the Applications directory.
• Linux and SUN: Type vmd in a terminal window.
• Windows: Select Start $\rightarrow$ Programs $\rightarrow$ VMD.

When VMD starts, by default three windows will open (Fig. 2): the VMD Main window, the OpenGL Display window, and the VMD Console window (or a Terminal window on a Mac). To end a VMD session, go to the VMD Main window, and choose File $\rightarrow$ Quit. You can also quit VMD by closing the VMD Console window or the VMD Main window.

Figure 2: The VMD Main window, the OpenGL Display window, and the VMD Console window.

Tutorial Topics and Files

The tutorial contains six sections. Each section acts as an independent tutorial for a specific topic, with the section layout as shown in Contents. For readers with no prior experience with VMD, we suggest they work through the sections in the order they are presented. For readers already familiar with the basics of VMD, they may selectively pursue sections of their interest. Several files have been prepared to accompany this tutorial. You need to download these files at http://www.ks.uiuc.edu/Training/Tutorials/vmd. The files needed for each chapter is illustrated in Fig. 3.

Figure 3: The files needed for each section. All files are contained in the vmd-tutorial-files folder, which can be downloaded from http://www.ks.uiuc.edu/Training/Tutorials/vmd.