Visual Molecular Dynamics

Visual Molecular Dynamics (VMD) is a molecular visualization and analysis software used to study the structure and dynamics of biological molecules such as proteins, nucleic acids, and lipids. It was developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign.

VMD allows users to visualize and analyze molecular structures in 3D. It can read and display various file formats, including PDB, MOL2, and XYZ, and can also read trajectory files from molecular dynamics simulations. Users can manipulate the visualization of the molecules, such as changing the colors, rendering styles, and displaying electrostatic potential surfaces.

In addition to visualization, VMD also has a wide range of analysis tools. These include tools to calculate distances, angles, torsions, and hydrogen bonds, as well as tools for clustering and principal component analysis. VMD also has scripting capabilities, allowing users to automate repetitive tasks and customize their analysis workflows.

VMD is widely used in the biomolecular research community and has been cited in numerous scientific publications. It is freely available for download and use on multiple platforms, including Windows, Mac, and Linux.