Contents

• List of Figures
• List of Tables
• Introduction
  • Contacting the authors
  • Registering VMD
  • Citation Reference
  • Acknowledgments
  • Copyright and Disclaimer Notices
  • For information on our other software
  
  
• Hardware and Software Requirements
  • Basic Hardware and Software Requirements
  • Multi-core CPUs and GPU Acceleration
  • Parallel Computing on Clusters and Supercomputers
  
  
• Tutorials
  • Rapid Introduction to VMD
  • Viewing a molecule: Myoglobin
  • Rendering an Image
  • A Quick Animation
  • An Introduction to Atom Selection
  • Comparing Two Structures
  • Some Nice Represenations
  • Saving your work
  • Tracking Script Command Versions of the GUI Actions
  
  
• Loading A Molecule
  • Notes on common molecular file formats
  • What happens when a file is loaded?
  • Babel interface
  • Raster3D file format
  
  
• User Interface Components
  • Using the Mouse in the Graphics Window
    • Mouse Modes
    • Pick Modes
    • Hot Keys
  • Using the Spaceball in the Graphics Window
    • Spaceball Driver
  • Using the Joystick in the Graphics Window
  • Description of each VMD window
    • Main Window
    • Main Window Molecule List browser
    • Main Window Animation Controls
    • Molecule File Browser Window
    • Mouse Menu
    • Display Menu and Display Settings Window
    • Graphics Window
    • Labels Window
    • Color Window
    • Material Window
    • Render Window
    • Tool Window
    • IMD Connect Simulation Window
    • Sequence Window
    • RamaPlot
  
  
• Molecular Drawing Methods
  • Rendering methods
    • Lines
    • Bonds
    • DynamicBonds
    • HBonds
    • Points
    • VDW
    • CPK
    • Licorice
    • Polyhedra
    • Trace
    • Tube
    • Ribbons
    • NewRibbons
    • Cartoon
    • NewCartoon
    • PaperChain
    • Twister
    • QuickSurf
    • Surf
    • MSMS
    • NanoShaper
    • VolumeSlice
    • Isosurface
    • FieldLines
    • Orbital
    • Beads
    • Dotted
    • Solvent
  • Coloring Methods
    • Color categories
    • Coloring Methods
    • Coloring by color categories
    • Color scale
    • Materials
  • Selection Methods
    • Definition of Keywords and Functions
    • Boolean Keywords
    • Short Circuiting
    • Quoting with Single Quotes
    • Double Quotes and Regular Expressions
    • Comparison selections
    • Comparison Operators
    • Other selections
  
  
• Viewing Modes
  • Perspective/Orthographic views
  • Monoscopic Modes
  • Stereoscopic Modes
    • Quad-buffered Stereo
    • Side-By-Side and Cross-Eyed Stereo
    • HDTV Side-by-side Stereo
    • Checkerboard Stereo
    • Column Interleaved Stereo
    • Row Interleaved Stereo
    • Anaglyph Stereo
    • Stereo Parameters
  
  
• Scene Export and Rendering
  • Screen Capture Using Snapshot
  • Higher Quality Rendering
  • Caveats
  • One Step Printing
  • Making Stereo Images
  • Making a Movie
  
  
• Tcl Text Interface
  • Using text commands
  • Tcl/Tk
  • Tcl Text Commands
    • animate
    • atomselect
    • axes
    • color
    • colorinfo
    • display
    • draw
    • exit
    • graphics
    • gettimestep
    • help
    • imd
    • label
    • light
    • logfile
    • material
    • mdffi
    • measure
    • menu
    • mol
    • molecule
    • molinfo
    • mouse
    • parallel
    • play
    • quit
    • render
    • rock
    • rotate
    • scale
    • stage
    • tool
    • translate
    • user
    • vmdinfo
    • volmap
    • voltool
    • wait
    • sleep
  • Tcl callbacks
  
  
• Python Text Interface
  • Using the Python interpreter within VMD
  • Python modules within VMD
  • Atom selections in Python
    • The built-in atomsel type
    • The AtomSel class (DEPRECATED)
    • An atom selection example
    • Changing the selection and the frame
    • Combining atom selections
    • RMS example
  • Python callbacks
    • Using Tkinter menus in VMD
  • Controlling VMD from Python
    • animate
    • axes
    • color
    • display
    • evaltcl
    • graphics
    • imd
    • label
    • material
    • measure
    • molecule
    • molrep
    • render
    • topology
    • trans
    • vmdnumpy
  • High-level Python Interface
    • Molecule
    • MoleculeRep
    • Draw Style Methods
    • Saving and Restoring Molecule State
  
  
• Vectors and Matrices
  • Vectors
  • Matrix routines
  • Multiplying vectors and matrices
  • Misc. functions and values
  
  
• Molecular Analysis
  • Using the molinfo command
  • Using the atomselect command
  • Analysis scripts
  • RMS Fit and Alignment
    • RMS Fit and Alignment Extension
    • RMS and scripting
  • VMD Script Commands for Colors
    • Changing the color scale definitions
    • Creating a set of black-and-white color definitions
    • Revert all RGB values to defaults
    • Coloring Trick - Override a Coloring Category
  
  
• Collective Variables Interface (Colvars)
  • Overview
  • Writing a Colvars configuration: a crash course
  • The Colvars dashboard
    • A mini-tutorial
    • The Dashboard window
    • Loading / Saving configuration files
    • The configuration editor
    • Plotting and visualizing collective variables
  • Enabling and controlling the Colvars module in VMD
    • Units in the Colvars module
    • Using the cv command to control the Colvars module
    • Configuration syntax used by the Colvars module
    • Global keywords
    • Input state file
    • Output files
  • Defining collective variables
    • Choosing a function
    • Distances
    • Angles
    • Contacts
    • Collective metrics
    • Rotations
    • Protein structure descriptors
    • Raw data: building blocks for custom functions
    • Geometric path collective variables
    • Arithmetic path collective variables
    • Shared keywords for all components
    • Periodic components
    • Non-scalar components
    • Linear and polynomial combinations of components
    • Scripted functions
    • Defining grid parameters
    • Trajectory output
    • Extended Lagrangian
    • Multiple time-step variables
    • Backward-compatibility
    • Statistical analysis
  • Selecting atoms
    • Atom selection keywords
    • Moving frame of reference.
    • Treatment of periodic boundary conditions.
    • Performance of a Colvars calculation based on group size.
  • Biasing and analysis methods
    • Thermodynamic integration
    • Adaptive Biasing Force
    • Extended-system Adaptive Biasing Force (eABF)
    • Metadynamics
    • Harmonic restraints
    • Computing the work of a changing restraint
    • Harmonic wall restraints
    • Linear restraints
    • Adaptive Linear Bias/Experiment Directed Simulation
    • Multidimensional histograms
    • Probability distribution-restraints
    • Defining scripted biases
    • Performance of scripted biases
  • Scripting interface (Tcl): list of commands
    • Commands to manage the Colvars module
    • Commands to manage individual collective variables
    • Commands to manage individual biases
  • Syntax changes from older versions
  
  
• Customizing VMD Sessions
  • VMD Command-Line Options
  • Environment Variables
  • Startup Files
    • Core Script Files
    • User Script Files
    • .vmdrc and vmd.rc Files
  • Using VMD as a WWW Client (for chemical/* documents)
    • MIME types
    • Setting up your .mailcap
    • Example sites
  
  
• Bibliography
• Index
• About this document ...