Programs that use or work with VMD
VMD can be used to perform visualization and analysis tasks in concert with other databases and software packages. The packages and web sites listed below directly support and/or directly use VMD.
- Bendix - analyze helix geometry
- PROPKA - VMD protein and protein-ligand pKa prediction GUI plugin for running PROPKA
- VMD-XPLOR - NMR visualization
- SurfVol - molecular surface and volume analysis
- OpenMM Zephyr - molecular simulation workflow tool that interfaces with VMD
- VsLab docking and virtual screening with VMD
- FeMD molecular dynamics simulation preparation tool
- vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD
- HOLE Suite: tools for visualization and analysis of pores in ion channels
- Interactive display of PDB structures with broad-illumination rendering
- TimeScapes molecular dynamics conformational change analysis package
- HiMach parallel molecular dynamics analysis framework
- Investigating Interfaces of Macro-Molecular Complexes with Intervor
- Dynamite bioinformatics server
- SBGrid - Structural Biology Grid
- ESPResSo - Software package for coarse-grained MD simulations
- Hase Group Simulation Movie Server
- MMTK - Molecular Modeling Toolkit
- Protein Folding and Unfolding Simulation Data Repository
- STRAP - Editor for Multiple Sequence Alignments
