VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. The program 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 large biomolecular complexes and long-timescale molecular dynamics trajectories, its interoperability with a large number of molecular dynamics simulation tools, its integration of structure and sequence information, and its built-in support for advanced image rendering and movie making.
Key features of VMD include:
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, animating and analyzing molecular dynamics simulation trajectories, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.
Before staring the tutorial you need to download the current version of VMD.
This tutorial requires VMD version 1.9.2 or later.
VMD supports all major computer platforms and can be obtained from the VMD
http://www.ks.uiuc.edu/Research/vmd. Follow the instruction online to install VMD in your computer. Once VMD is installed, to start VMD:
The tutorial contains six sections. Each section acts as an independent tutorial for a specific topic, with the section layout as shown in Contents. We suggest that readers with no prior VMD experience work through the sections in the order they are presented. Readers already familiar with the basics of VMD 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 are illustrated in Fig. 3.