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)
- Intersurf — Display interaction surfaces between two groups of atoms
- 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/...)
- PMEpot — Particle Mesh Ewald potential map calculator
- RamaPlot — Ramachandran plots for selected atoms
- RMSD Tool — Calculate RMSD values
- RMSD Trajectory Tool — Extended version of RMSD plugin for trajectories
- Salt Bridges — Find salt bridges throughout a trajectory
- Timeline — Plot time-varying secondary structure
- VolMap — Graphical front-end for the VMD VolMap command
- Sequence Viewer — Browse sequences of loaded molecules
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
- STING — Query STING database by PDB code
- Text Viewer — Display text files
Modeling
- AutoIonize — Add sodium or chlorine ions to a structure for simulation
- AutoPSF — Automatic PSF structure building tool
- CGTools — Transform structures between coarse-grain and all-atom representations
- Dowser — Add water to a structure for simulation, using Dowser
- Membrane — Build POPC or POPE membranes
- Molefacture — structure builder (used by paratool/autopsf/etc)
- Mutator — Mutate residues
- Paratool — Calculation of force field parameters
- Psfgen — Build structures for use with NAMD
- Solvate — Add water to a structure for simulation
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
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
- PBCTools — Tools for manipulating simulation data with periodic boundary conditions
- RESPTool — Paratool helper, graphical interface for running RESP jobs
- Optimization — Multidimensional minimization of functions
- TkCon — Text console with syntax highlighting and command history
Third-Party VMD Plugins and Extensions:
VMD Python Library Binaries for VMD 1.8.x
Plugin updates