In addition to Tcl and Python scripts, VMD implements "plugin" interfaces which provide a means for extending VMD at run-time without the necessity to recompile the program. The two primary types of plugins for VMD are 'molfile' plugins for reading and writing data files containing atomic, graphics, and volumetric data, and scripting extensions which implement new commands and user interfaces for performing tasks such as structure building, simulation setup, etc. This page contains plugins which can be downloaded and installed in your copy of VMD, as well as any pertinent documentation that goes along with the plugins.

License

The VMD plugins are provided under the UIUC Open Source License, any exceptions are explicitly marked as such.

Plugin Developer Documentation:

  • Plugin Programmer's Guide — describes the VMD plugin architecture so others can develop and build new plugins, and to use the VMD plugins in other software

Molfile Plugin Documentation:

Extensions Documentation:

Analysis
  • APBSRun — Calculate electrostatic potentials using APBS
  • CatDCD — Standalone trajectory processing program
  • Contact Map — Plot a 2-d residue-residue distance map
  • GofRGUI — Calculate and plot radial pair distribution functions g(r)
  • HBonds — Counts the number of hydrogen bonds formed over a trajectory
  • HeatMapper — Plot 2-D heat maps of 3-D values with a color scale bar
  • ILSTools — Prepare and run Implicit Ligand Sampling (ILS) calculations
  • IRSpecGUI — IR spectral density calculator
  • MultiSeq — Perform multiple sequence and multiple structure alignments, display sequence data, phylogenetic trees, and much more.
  • NAMD Energy — Evaluate interaction energies with NAMD
  • NAMD Plot — Plot NAMD log files (energy/volume/...)
  • NetworkView — View protein interaction networks
  • NMWiz — Normal mode visualization and comparative analysis
  • ParseFEP — Analyze NAMD free-energy purturbation (FEP) Simulations
  • PMEpot — Particle Mesh Ewald potential map calculator
  • PropKa GUI — graphical interface for PROPKA
  • RamaPlot — Ramachandran plots for selected atoms
  • RMSD Tool — Calculate RMSD values
  • RMSD Trajectory Tool — Extended version of RMSD plugin for trajectories
  • RMSD Visualizer Tool — Tool for aligning selections and measuring and plotting RMSD and RMSF values over trajectories
  • Salt Bridges — Find salt bridges throughout a trajectory
  • Sequence Viewer — Browse sequences of loaded molecules
  • Symmetry Tool — Determine the symmetry pointgroup of an atom selection and display the symmetry elements
  • Timeline — Plot time-varying secondary structure
  • VolMap — Graphical front-end for the VMD VolMap command
BioCoRE Collaboration Tools
  • Chat — Chat with other BioCoRE users from within VMD
  • Login — Login to BioCoRE from within VMD
  • Shared VMD Views — Publish and view VMD states to/from other BioCoRE users
Data Importing and Plotting
  • Data Import — Load per-residue values into the "beta" column of a PDB file
  • Multiplot — Scriptable data plotting tool
  • PDBtool — Query various information about PDB structures
  • MultiText — Display and edit text files
Modeling
  • AutoIonize — Add sodium or chlorine ions to a structure for simulation
  • AutoPSF — Automatic PSF structure building tool
  • Chirality — Detect and fix chirality errors in protain and nucleic acid structures
  • Cispeptide — Detect, visualize, and fix cis peptide bonds in protein structures
  • CGTools — Transform structures between coarse-grain and all-atom representations
  • Dowser — Add water to a structure for simulation, using Dowser
  • FFTK — Tool to aid users in the development of CHARMM-compatible force field parameters
  • Inorganic Builder — Build inorganic structures
  • MDFF — Flexibly fit atomic structures into density maps
  • Membrane — Build POPC or POPE membranes
  • MergeStructs — Merge multiple structures
  • Molefacture — structure builder (used by paratool/autopsf/etc)
  • Mutator — Mutate residues
  • Nanotube — Build single-wall carbon nanotubes
  • Paratool — Calculation of force field parameters
  • Psfgen — Build structures for use with NAMD
  • Solvate — Add water to a structure for simulation
  • SSRestraints — Generate secondary structure restraints for use with NAMD
  • Topotools — Manipulate topology related properties
Simulation
  • AutoIMD — Setup and run Interactive Molecular Dynamics simulations
  • IMDMenu — Monitor status of running Interactive Molecular Dynamics simulaions
  • NAMD GUI — graphical interface for setting up and running NAMD jobs
  • NAMD Server — an programming interface for starting NAMD in "server mode"
  • QMTool — Graphical interface for setting up QM jobs
Visualization
  • Clipping Plane Tool — Clipping plane controls
  • Clone Rep — Clone sets of representations
  • Dipole Watcher — Animate selected dipole moments
  • Intersurf — Display interaction surfaces between two groups of atoms
  • Navigate — Keyboard camera navigation
  • NavFly — Mouse-based flying camera navigation
  • MultiMolAnim — Animation of multiple molcules or time-varying topologies
  • Color Scale Bar — Draw a bar for the current color scale
  • Remote — VMD phone/tablet remote control management interface
  • Palette Tool — Display active colors and materials, for test rendering and printing
  • ViewChangeRender — Easy-to-use camera flight movies
  • Viewmaster — Manage sets of structure views within VMD
  • Virtual DNA Viewer — Draw DNA representation from helical parameters
  • VMDMovie — Create MPEG and AVI movies for presentations
Other
  • AtomEdit — Atom property editor, used by other plugins
  • DemoMaster — Tool for giving live and pre-scripted VMD demos
  • ExecTool — Local and remote job execution and executable finder plugin used by other tools
  • Hesstrans — Paratool helper, transforms hessian matrix into internal coords
  • Optimization — Multidimensional minimization of functions
  • PBCTools — Tools for manipulating simulation data with periodic boundary conditions
  • RESPTool — Paratool helper, graphical interface for running RESP jobs
  • RNAview — SSRestraints helper, uses the program RNAView for secondary structure analysis of nucleic acids
  • SignalProc — Signal processing utilities (e.g.FFT)
  • TkCon — Text console with syntax highlighting and command history

Externally-hosted VMD Plugins and Extensions:

  • Check Sidechains Plugin — checks and helps select best orientation and protonation state for Asn, Gln, and His side chains
  • MultiMSMS Plugin — caches MSMS calculations to speedup the animation of a sequence of rames
  • Interactive Essential Dynamics — Interactive visualization of essential dynamics
  • Mead Ionize — Improved version of autoionize for highly charged systems
  • Andriy Anishkin's VMD Scripts — Many useful VMD scripts for visualization and analysis
  • RMSD Trajectory Tool — Development version of RMSD plugin for trajectories
  • Clustering Tool — Visualize clusters of conformations of a structure
  • iTrajComp — interactive Trajectory Comparison tool
  • Swap — Atomic coordinate swapping for improved RMSD alignment
  • Intervor — Protein-Protein interface extraction and display
  • SurfVol — Measure surface area and volume of proteins
  • vmdICE — Plugin for computing RMSD, RMSF, SASA, and other time-varying quantities

VMD Python Library Binaries for VMD 1.8.x

Plugin updates