(Visual Molecular Dynamics) is an interactive molecular visualization and analysis program designed for biomolecules. It runs on a variety of platforms including Windows, Mac OS X, and Linux. VMD
provides a wide range of features for the analysis of biomolecular systems, including:
1. Molecular Dynamics Simulations: VMD supports an extensive range of atom-based and coarse-grained molecular dynamics simulations, including those using CHARMM, AMBER, and NAMD. It is also capable of creating trajectory files in various formats, including the widely used DCD (dynamic coordinate) file format.
2. Graphical User Interface: VMD has a sophisticated graphical user interface (GUI) which is highly customizable and intuitive to use. The GUI makes it easy to navigate complex molecular dynamics simulations, visualize them in 3D, and analyze the data.
3. Molecular Visualization: VMD provides a range of powerful visualization tools, including the ability to create high-resolution images and videos of molecular structures and dynamic processes.
4. Analysis Tools: VMD includes a set of analysis tools for molecular dynamics simulations, including the ability to calculate the free energy of proteins and ligands, the ability to analyze electrostatic potentials, and the ability to measure distances and angles between atoms.
5. Molecular Manipulation: VMD includes a set of tools for manipulating molecules, including the ability to rotate, translate, and scale molecules, as well as the ability to add/remove atoms and bonds.
6. Molecular Design: VMD includes a set of tools for designing molecules, including the ability to create and optimize protein structures, and the ability to perform ligand-based virtual screening.
7. Molecular Interaction Networks: VMD includes a set of tools for creating and visualizing molecular interaction networks, including the ability to view hydrogen bonds, electrostatic interactions, and van der Waals interactions.
8. Molecular Scripting: VMD includes an integrated scripting language, allowing users to write custom scripts to automate tasks and extend the functionality of VMD.
9. Web Services: VMD includes a set of web service APIs, allowing users to interact with VMD from remote locations and access the VMD program from the web.
VMD enables the visualization of molecular structures, dynamic processes, and their physical properties in detail.