Using VMD: An Introductory Tutorial
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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
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PDF or HTML at Wiley Online LibraryTable 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
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Figure 5.7.1 Example renderings made with VMD (Cruz‐Chu et al., ; Freddolino et al., ; Yin et al., ; Yu et al., ; Sotomayor et al., ; Wang et al., ). View Image -
Figure 5.7.2 Loading a molecule. View Image -
Figure 5.7.3 Rotational modes. (A ) Rotation axes when holding down the left mouse key. (B ) The rotation axes when holding down the right mouse key. View Image -
Figure 5.7.4 Mouse modes and their characteristic cursors. View Image -
Figure 5.7.5 The Graphical Representations window. (A ) List of representations, (B ) the tabs for Draw Style, Selections, Trajectory, and Periodic, (C ) Coloring Method pull‐down menu, (D ) Drawing Method pull‐down menu, (E ) user‐adjustable parameters for different drawing methods, and (F ) selection text entry box. View Image -
Figure 5.7.6 (A ) Licorice, (B ) Tube, and (C ) NewCartoon representations of ubiquitin. View Image -
Figure 5.7.7 Graphical Representations window and the (A ) Selections tab, (B ) list of Singlewords, (C ) list of Keywords, and (D ) Value box that displays possible choices for a given keyword. View Image -
Figure 5.7.8 Multiple Representations of ubiquitin. Representations can be either created or deleted using the (A ) Create Rep and (B ) Delete Rep buttons. Screen also shows (C ) the Material pull‐down menu and (D ) list of representations. View Image -
Figure 5.7.9 (A ) The VMD Sequence window displays properties of the protein sequence, including (B ) the B‐value and (C ) the secondary structure, denoted by (D ) the color codes. (E ) The list of residues is displayed, with the selected residues highlighted in yellow. (F ) Zoom controls are also shown in the window. View Image -
Figure 5.7.10 The effect of the resolution setting. (A ) Low resolution: Sphere Resolution set to 8. (B ) High resolution: Sphere Resolution set to 28. View Image -
Figure 5.7.11 Examples of different material settings. (A ) The default transparent material, rendered in GLSL mode. (B ) A user‐defined material with high transparency, also rendered in GLSG mode. View Image -
Figure 5.7.12 Comparison of the (A ) perspective and (B ) orthographic projection modes. View Image -
Figure 5.7.13 Stereo image of the ubiquitin protein. Shown here with Cue Mode = Linear, Cue Start = 1.5, and Cue End = 2.75. To view the stereo image, use the “wall‐eyed” method: hold the page close to eyes, and shift the focus beyond the page until the two images overlap to form a three‐dimensional object. If this is difficult, try scaling down the figure to a smaller size. This will make viewing easier. View Image -
Figure 5.7.14 Example of a POV3 rendering. View Image -
Figure 5.7.15 Animation tools in the VMD main menu. The tools allow one to go over frames of the trajectory (e.g., using the “slider”) and to play a movie of the trajectory in various modes (Once, Loop, or Rock) and at an adjustable speed. View Image -
Figure 5.7.16 Image of every tenth frame shown at once, smoothed with a 20‐frame window. View Image -
Figure 5.7.17 Water within 3 Å of the protein, shown for a selection that is not updated (A ) and for the one that is updated (B ) each frame. The snapshots shown are (from left to right) for frames 0, 17, and 99. View Image -
Figure 5.7.18 Ubiquitin in the VDW representation, colored according to the hydrophobicity of its residues. View Image -
Figure 5.7.19 The Molecule List Browser. View Image -
Figure 5.7.20 Result of the alignment between the two aquaporins using the measure fit command. View Image -
Figure 5.7.21 VMD Main menu after loading the four aquaporins. View Image -
Figure 5.7.22 The four aquaporins aligned according to their structural similarity. View Image -
Figure 5.7.23 Result of a structural alignment of the four aquaporins, colored by Qres . View Image -
Figure 5.7.24 Result of a sequence alignment of the four aquaporins, colored by sequence identity. View Image -
Figure 5.7.25 Top view of the aligned aquaporins colored by sequence conservation. The conserved residues locate mostly inside the aquaporin pore. View Image -
Figure 5.7.26 (A ) A structure‐based phylogenetic tree generated by QH values. (B ) A sequence‐based phylogenetic tree generated by ClustalW. View Image -
Figure 5.7.27 Labels in VMD. View Image -
Figure 5.7.28 RMSD Trajectory Tool. The RMSD is plotted for the equilibration of ubiquitin. View Image -
Figure 5.7.29 RMSD versus time for the equilibration (blue) and pulling (red) trajectories of ubiquitin. View Image -
Figure 5.7.30 Distance between a residue and the center of ubiquitin. The distances analyzed are those for residue 76 (black) and residue 10 (green). View Image
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 |
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