Quick Guide

File controls

Load and Save Structures and Trajectories with a few clicks!

The new "Load Structure & Trajectory" button in VMD 2.0 makes it easier than ever to visualize your molecular data. With just one click, you can load structures and trajectories from the most widely used biomolecular simulation packages, including: CHARMM/NAMD (.psf, .dcd), GROMACS (.gro, .xtc, .trr, .tpr), AMBER (.prmtop, .inpcrd, .mdcrd, .nc), Maestro/Desmond (.cms, .mae,.drt) , and Quantum Chemistry: Gaussian, GAMESS, VASP. VMD’s powerful molfile plugin ensures broad compatibility with the most widely used formats.

Scripting to take your molecular visualization and analysis to the next level.

Tcl and Python scripting Interface

With a Turing-complete command-line interface, you can fully automate your workflows, integrate VMD into larger computational pipelines, and create custom analysis tools for your research. You get programmatic access to:
* All particle coordinates & properties for advanced analysis.
*Powerful atom selections with flexible queries
* Automated measurements for distances, angles, RMSD, and more Direct access to plugins for trajectory analysis, QM/MM workflows, and enhanced visualization
* Enhanced Python support is coming in the final VMD 2.0 release! Get ready for deeper integration with modern scientific Python libraries.

Stunning Images & Movies for Scientific Publications

Image/Movie Rendering tools

Creating high-quality molecular visuals has never been easier. The new Magic Wand button—an intelligent, content-aware tool—instantly refines your visualization, making structures presentation-ready with a single click. Currently optimized for protein-ligand systems, this feature automatically applies the best rendering styles, colors, and representations to enhance clarity and aesthetics.
For those who love fine-tuning their visuals, VMD 2.0 provides deep control over display settings. Adjust Shadows, Ambient Occlusion, and Depth of Field to create lifelike molecular renderings with stunning depth and realism.
Whether you're preparing figures for a high-impact journal, crafting animations for presentations, or generating movies of your simulations, VMD 2.0 delivers unmatched flexibility and quality.

Intuitive Measurements & Seamless View Management

Quick access to common measurements

Understanding molecular interactions is easier than ever with VMD 2.0’s new measurement buttons. Dedicated buttons let you instantly measure distances, angles, and torsions, making structural analysis effortless. Even better, you can plot these properties over a trajectory, allowing you to track their dynamic behavior in real time. Whether you're analyzing conformational changes, ligand binding, or protein flexibility, VMD 2.0 puts the data at your fingertips. ViewMaster comes handy for seamless presentations and rapid structure annotations. ViewMaster tool lets you save and restore viewpoints and visual representations with a single click. No more manually resetting views—jump between key perspectives, highlight interactions, and prepare figures effortlessly. Whether you're presenting your research or refining molecular scenes for publication, ViewMaster accelerates your workflow

Controls for Interactive Molecular Exploration

Touchscreen controls

Experience molecular exploration at your fingertips. VMD 2.0 introduces a new level of interactivity with four dedicated buttons designed for touchscreen devices and interactive displays. Navigating molecular structures is now more intuitive than ever. You can effortlessly rotate your structure with precision, translate molecules with a simple touch, center the rotation on a key region for focused exploration, and reset the view instantly when needed. Combined with the ViewMaster, these tools make VMD 2.0 the perfect choice for interactive presentations, scientific exhibits, and real-time discussions. Whether you're using a touchscreen monitor, a tablet, or a large interactive display, molecular visualization becomes smooth, natural, and engaging.

Tools for Sequence Analysis, Structural Alignment, and Molecular Interactions

Alignment and Interactions

Tools for Sequence Analysis, Structural Alignment, and Molecular Interactions
The Sequence Viewer displays protein residues and nucleic acid bases, allowing direct selection and highlighting in the 3D structure. MultiSeq enables sequence and structural alignment, helping users compare proteins and nucleic acids efficiently.The RMSDTT tool enhances RMSD calculations by allowing frame skipping, all-to-all RMSD comparisons, weighted RMSD, and trajectory alignment. Results can be plotted in VMD or exported for further analysis.The H-bonds plugin tracks hydrogen bond formation over a trajectory, counting interactions within a selection or between two selections. It provides detailed output on bond persistence and interaction frequencies, with results displayed in VMD or saved to a file.

Molecular Dynamics Made Easy

QwikMD

QwikMD simplifies the process of setting up molecular dynamics simulations, connecting VMD with NAMD to provide an easy interface for users, especially beginners or experimentalists. With QwikMD, users can quickly run simulations to explore protein mutations, deletions, or even perform steering experiments. It streamlines the MD workflow by automating key steps, checking for errors, and ensuring reproducibility. The tool also includes info buttons to explain the theoretical background behind each procedure, making it an excellent learning tool.

Collective Variables Dashboard

Colvars

Colvars allows for advanced analysis by reducing complex systems into key parameters, called collective variables (colvars), that capture the system’s most important behaviors. This module can be used to apply biasing potentials, calculate potentials of mean force (PMFs), and analyze statistical properties of colvars. Users can perform tasks like enhanced sampling with methods such as Adaptive Biasing Force (ABF), metadynamics, umbrella sampling, and more, either during or after a simulation. Colvars also supports multidimensional histograms and other analyses to help researchers gain insights from their simulations with ease.