Using VMD: An introductory tutorial

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assem-blies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.