Using VMD: An Introductory Tutorial

Jen Hsin1, Anton Arkhipov1, Ying Yin1, John E. Stone1, Klaus Schulten1

1 Beckman Institute, University of Illinois at Urbana‐Champaign, Urbana, Illinois
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 5.7
DOI:  10.1002/0471250953.bi0507s24
Online Posting Date:  December, 2008
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

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. Curr. Protoc. Bioinform. 24:5.7.1‐5.7.48. © 2008 by John Wiley & Sons, Inc.

Keywords: molecular modeling; molecular dynamics visualization; interactive visualization; animation

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Downloading VMD
  • Topics and Files
  • Working with a Single Molecule
  • Basic Protocol 1: Loading and Displaying the Molecule
  • Basic Protocol 2: The Basics of VMD Figure Rendering
  • Working with Trajectories and Making Movies
  • Basic Protocol 3: Working with Trajectories
  • Basic Protocol 4: The Basics of Movie Making in VMD
  • Scripting in VMD
  • Basic Protocol 5: The Basics of Tcl Scripting
  • Basic Protocol 6: Working with a Molecule Using Tcl Text Commands
  • Basic Protocol 7: Sourcing Scripts
  • Basic Protocol 8: Drawing Shapes Using VMD Text Commands
  • Working with Multiple Molecules
  • Basic Protocol 9: Molecule List Browser
  • Basic Protocol 10: Aligning Molecules with the measure fit Command
  • Comparing Protein Structures and Sequences with the MultiSeq Plugin
  • Basic Protocol 11: Structure Alignment with MultiSeq
  • Basic Protocol 12: Sequence Alignment with MultiSeq
  • Basic Protocol 13: Creating a Phylogenetic Tree with MultiSeq
  • Data Analysis in VMD
  • Basic Protocol 14: Adding Labels in VMD
  • Basic Protocol 15: Example of a Built‐In Analysis Tool: The RMSD Trajectory Tool
  • Basic Protocol 16: Example of an Analysis Script
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

   Cruz‐Chu, E.R., Aksimentiev, A., and Schulten, K. 2006. Water‐silica force field for simulating nanodevices. J. Phy. Chem. B. 110:21497‐21508.
   Eastwood, M.P., Hardin, C., Luthey‐Schulten, Z., and Wolynes, P.G. 2001. Evaluating protein structure‐prediction schemes using energy landscape theory. IBM J. Res. Dev. 45:475‐497.
   Freddolino, P.L., Arkhipov, A.S., Larson, S.B., McPherson, A., and Schulten, K. 2006. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14:437‐449.
   Frishman, D. and Argos, P. 1995. Knowledge‐based secondary structure assignment. Proteins 23:566‐579.
   Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD–Visual Molecular Dynamics. J. Mol. Grap. 14:33‐38.
   Isralewitz, B., Gao, M., and Schulten, K. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11:224‐230.
   Murata, K., Mitsuoka, K., Hirai, T., Walz, T., Agre, P., Heymann, J.B., Engel, A., and Fujiyoshi, Y. 2000. Structural determinants of water permeation through aquaporin‐1. Nature 407:599‐605.
   Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781‐1802.
   Roberts, E., Eargle, J., Wright, D., and Luthey‐Schulten, Z. 2006. MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics. 7:382.
   Russell, R.B. and Barton, G.J. 1992. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and resiude confidence levels. Proteins 14:309‐323.
   Savage, D.F., Egea, P.F., Robles‐Colmenares, Y., O'Connell, J.D. III, and Stroud, R.M. 2003. Architecture and selectivity in aquaporins: 2.5 Å X‐ray structure of aquaporin Z. PLoS Biol. 1:E72.
   Sotomayor, M., Vasquez, V., Perozo, E., and Schulten, K. 2007. Ion conduction through MscS as determined by electrophysiology and simulation. Biophys. J. 92:886‐902.
   Sui, H., Han, B.‐G., Lee, J.K., Walian, P., and Jap, B.K. 2001. Structural basis of water‐specific transport through the AQP1 water channel. Nature 414:872‐878.
   Tajkhorshid, E., Nollert, P., Jensen, M.Ø., Miercke, L.J.W., O'Connell, J., Stroud, R.M., and Schulten, K. 2002. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296:525‐530.
   Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673‐4680.
   Törnroth‐Horsefield, S., Wang, Y., Hedfalk, K., Johanson, U., Karlsson, M., Tajkhorshid, E., Neutze, R., and Kjellbom, P. 2006. Structural mechanism of plant aquaporin gating. Nature 439:688‐694.
   Vijay‐Kumar, S., Bugg, C.E., and Cook, W.J. 1987. Structure of ubiquitin at 1.8Å resolution. J. Mol. Biol. 194:531‐544.
   Wang, Y., Cohen, J., Boron, W.F., Schulten, K., and Tajkhorshid, E. 2007. Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J. Struct. Biol. 157:534‐544.
   Yin, Y., Jensen, M.Ø., Tajkhorshid, E., and Schulten, K. 2006. Sugar binding and protein conformational changes in lactose permease. Biophys. J. 91:3972‐3985.
   Yu, J., Yool, A.J., Schulten, K., and Tajkhorshid, E. 2006. Mechanism of gating and ion conductivity of a possible tetrameric pore in Aquaporin‐1. Structure 14:1411‐1423.
Supplemental Files
   Supplemental files can be downloaded from http://www.currentprotocols.com by clicking “Current Protocols” beneath the Bioinformatics head and following the Sample Datasets link.
  pdb coordinate file for human aquaporin (Murata et al., )
   1fqy.pdb
  pdb coordinate file for bovine aquaporin (Sui et al., )
   1j4n.pdb
  pdb coordinate file for E. coli GlpF (Tajkhorshid et al., )
   1lda.pdb
  pdb coordinate file for E. coli aquaporin (Savage et al., )
   1rc2.pdb
  pdb coordinate file for ubiquitin (Vijay‐Kumar et al., )
   1ubq.pdb
  An example tcl script.
   beta.tcl
  An example tcl script.
   distance.tcl
  dcd molecular dynamics trajectory file of an equilibration simulation
   equilibration.dcd
  dcd molecular dynamics trajectory file of a protein‐pulling simulation
   pulling.dcd
  An example fasta protein sequence file.
   spinach_aqp.fasta
  psf structure file for ubiquitin that defines connectivity of atoms
   ubiquitin.psf
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library