title: Using VMD: an introductory tutorial.
abstract: VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, 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.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Jen
authors.initials: J
authors.lastname: Hsin
authors.forename: Anton
authors.initials: A
authors.lastname: Arkhipov
authors.forename: Ying
authors.initials: Y
authors.lastname: Yin
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D010802:Phylogeny; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins