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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 Com- putational Biophysics Group at the University of Illinois at Urbana-Champaign.
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University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group
Computational Biophysics Workshop
Using VMD
VMD Developer:
John E. Stone
Tutorial Contributors:
Alek Aksimentiev, Anton Arkhipov, Reuven Birnbaum,
Robert Brunner, Jordi Cohen, Brijeet Dhaliwal, John Eargle,
Jen Hsin, Fatemeh Khalili, Eric H. Lee, Zan Luthey-Schulten,
Patrick O’Donoghue, Elijah Roberts, Anurag Sethi, Marcos So-
tomayor, John E. Stone, Emad Tajkhorshid, Leonardo Trabuco,
Elizabeth Villa, Yi Wang, David Wells, Dan Wright, Ying Yin
Apr. 2017
A current version of this tutorial is available at:
http://www.ks.uiuc.edu/Training/Tutorials/
Join the tutorial-l@ks.uiuc.edu mailing list for additional help.
CONTENTS 2
Contents
1 Working with a Single Molecule 7
1.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2 Displaying the Molecule . . . . . . . . . . . . . . . . . . . . . . . 8
1.3 Graphical Representations . . . . . . . . . . . . . . . . . . . . . . 9
1.3.1 Exploring different drawing styles . . . . . . . . . . . . . . 9
1.3.2 Exploring different coloring methods . . . . . . . . . . . . 11
1.3.3 Displaying different selections . . . . . . . . . . . . . . . . 12
1.3.4 Creating multiple representations . . . . . . . . . . . . . . 13
1.4 Sequence Viewer Extension . . . . . . . . . . . . . . . . . . . . . 15
1.5 Saving Your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.6 The Basics of VMD Figure Rendering . . . . . . . . . . . . . . . 17
1.6.1 Setting the display background . . . . . . . . . . . . . . . 17
1.6.2 Increasing resolution . . . . . . . . . . . . . . . . . . . . . 17
1.6.3 Colors and materials . . . . . . . . . . . . . . . . . . . . . 18
1.6.4 Depth perception . . . . . . . . . . . . . . . . . . . . . . . 20
1.6.5 Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2 Trajectories and Movie Making 25
2.1 Loading Trajectories . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.2 Main Menu Animation Tools . . . . . . . . . . . . . . . . . . . . 26
2.3 Trajectory Visualization . . . . . . . . . . . . . . . . . . . . . . . 27
2.3.1 Smoothing trajectories . . . . . . . . . . . . . . . . . . . . 27
2.3.2 Displaying multiple frames . . . . . . . . . . . . . . . . . 27
2.3.3 Updating selections . . . . . . . . . . . . . . . . . . . . . 28
2.4 The Basics of Move Making in VMD . . . . . . . . . . . . . . . . 29
2.4.1 Making single-frame movies . . . . . . . . . . . . . . . . . 30
2.4.2 Making trajectory movies . . . . . . . . . . . . . . . . . . 30
3 Scripting in VMD 32
3.1 The Basics of Tcl Scripting . . . . . . . . . . . . . . . . . . . . . 32
3.2 VMD scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2.1 Loading molecules with text commands . . . . . . . . . . 34
3.2.2 The atomselect command . . . . . . . . . . . . . . . . . 35
3.2.3 Obtaining and changing molecule properties with text
commands . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.2.4 Sourcing scripts . . . . . . . . . . . . . . . . . . . . . . . . 39
3.3 Drawing shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
CONTENTS 3
4 Working with Multiple Molecules 42
4.1 Main Menu Molecule List Browser . . . . . . . . . . . . . . . . . 42
4.1.1 Loading multiple molecules . . . . . . . . . . . . . . . . . 42
4.1.2 Changing molecule names . . . . . . . . . . . . . . . . . . 43
4.1.3 Drawing different representations for different molecules . 43
4.1.4 Molecule Status Flags . . . . . . . . . . . . . . . . . . . . 44
4.2 Aligning Molecules with the measure fit Command . . . . . . . 46
5 Comparing Structures and Sequences with MultiSeq 48
5.1 Structure Alignment with MultiSeq . . . . . . . . . . . . . . . . . 48
5.1.1 Loading aquaporin structures . . . . . . . . . . . . . . . . 48
5.1.2 Aligning the molecules . . . . . . . . . . . . . . . . . . . . 49
5.1.3 Coloring molecules by their structural identity . . . . . . 52
5.2 Sequence Alignment with MultiSeq . . . . . . . . . . . . . . . . . 52
5.2.1 Aligning molecules and coloring molecules by degree of
conservation . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.2.2 Importing FASTA files for sequence alignment . . . . . . 53
5.3 Phylogenetic Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
6 Data Analysis in VMD 58
6.1 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
6.2 Example of a built-in analysis tool: the RMSD Trajectory Tool . 60
6.3 Example of an analysis script . . . . . . . . . . . . . . . . . . . . 63
7 Running VMD on Supercomputers 68
7.1 Running VMD in Text Mode . . . . . . . . . . . . . . . . . . . . 68
7.2 Running VMD with Off-Screen OpenGL Graphics . . . . . . . . 69
7.3 Using VMD with MPI . . . . . . . . . . . . . . . . . . . . . . . . 71
7.4 VMD parallel commands . . . . . . . . . . . . . . . . . . . . . . . 72
CONTENTS 4
Introduction
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 Com-
putational 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 dynam-
ics trajectories, its interoperability with a large number of molecular dynamics
simulation tools, its integration of s tructure and sequence information, and its
built-in support for advanced image rendering and movie making.
Figure 1: Example VMD renderings.
Key features of VMD include:
• General 3- D molecular visualization with extensive drawing and coloring
methods and strong support for visualization of m olecular dynamics
• Supports all major molecular data file formats, with no limits to structure
or trajectory sizes except memory capacity and addressing
• Extensive atom selection syntax for choosing subsets of atoms for both
analytical tasks and for graphical display
• Visualization of volumetric data
• Molecular analysis commands
• Rendering of high-resolution, publication-quality molecule images
• Built-in movie making tools
• Building and preparing systems for molecular dynamics simulations
• Interactive molecular dynamics simulations
• User-extensible through the built-in Tc l and Python scripting languages
• Extensible source code written in C and C++
CONTENTS 5
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 visu-
alizing molecules in three dimensions with different drawing and coloring meth-
ods, rendering publication-quality figures, animating and analyzing molecular
dynamics simulation trajectories, scripting in the te xt-based Tcl/Tk interface,
and analyzing both sequence and s tructure data for proteins.
Downloading VMD
Before staring the tutorial you need to download the current version of VMD.
This tutorial requires VMD version 1.9.2 or later. VMD s upports all major
computer platforms and can be obtained from the VMD homepage
http://www.ks.uiuc.edu/Research/vmd. Follow the instruction online to install
VMD in your computer. Once VMD is installed, to start VMD:
• Mac OS X: Double click on the VMD application icon in the Applications
directory.
• Linux and other Unix platforms: Type vmd in a terminal window.
• Windows: Select Start → Programs → VMD.
When VMD starts, by default three windows will open (Fig. 2): the VMD Main
window, the OpenGL Display window, and the VMD Console window (or a
Terminal window on a Mac). To end a VMD session, go to the VMD Main
window, and choose File → Quit. You can also quit VMD by closing the VMD
Console window or the VMD Main window.
Figure 2: The VMD Main window, the OpenGL Display window, and the VMD
Console window.
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