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What is new in VMD 2

New User Interface

A Streamlined Interface for VMD 2.0

VMD 2.0 introduces a redesigned interface that significantly enhances usability, making molecular visualization more intuitive and efficient. A key improvement is the addition of new action buttons that provide quick access to commonly used features, reducing the need for complex menu navigation. The interface is now more accessible, with a cleaner layout and streamlined workflows that make it easier to apply, modify, and combine representations.

Selections and visual properties are now integrated directly into the main interface, eliminating the need for multiple windows and pop-ups. Users can quickly adjust rendering styles, colors, and transparency without breaking their workflow. The improved selection engine allows for faster, more precise molecular filtering based on atomic properties, residue types, secondary structures, and dynamic behaviors.

VMD 2.0 is also optimized for modern display technology, supporting touchscreens and ultra-high-definition screens, making interactions more seamless and responsive. The improved layout ensures that tools are easier to find and use, making molecular visualization smoother and more efficient than ever before.

New Secondary Structure Calculations

Fast and Scalable Secondary Structure Calculation in VMD 2.0

VMD 2.0 introduces a new, efficient method for calculating secondary structure, designed to handle large molecular systems with improved speed and scalability. Unlike traditional approaches, this new algorithm quickly assigns secondary structure based on Phi/Psi backbone angles and distance-based criteria, making it well-suited for analyzing dynamic changes in secondary structure over time.

This method provides a fast and responsive way to track secondary structure evolution in molecular dynamics simulations, allowing users to explore conformational shifts in real-time. Optimized for performance, it supports systems with up to ~1 million solute atoms, making it a valuable tool for studying large biomolecular assemblies without compromising speed or accuracy.

Glycan Visualization Tools

High-Performance Glycan Visualization in VMD 2.0

VMD 2.0 introduces a new SNFG-compliant GLYCAM representation, enhancing clarity and accuracy in glycan rendering. This update delivers an unprecedented speedup over 3D-SNFG, making large glycoprotein visualization vastly more efficient. For a COVID-19 spike protein (6M+ atoms), VMD 2.0 achieves a 10⁶ times performance boost, enabling real-time exploration of glycan dynamics and interactions at an unprecedented scale.

Enhanced Surface Visualization

Fast and Efficient Surface Calculations in VMD 2.0

VMD 2.0 features a new surface calculation algorithm that is 10× faster than previous versions, enabling rapid visualization of large biomolecular assemblies. Optimized for high-performance computing, it ensures smooth, real-time rendering, even on ultra-high-definition displays, making molecular surface analysis faster and more efficient than ever.

Live rendering mode

Live Ray Tracing in VMD 2.0

VMD 2.0 introduces real-time ray tracing, delivering high-quality molecular rendering with interactive lighting, shadows, and reflections. Optimized for modern GPUs and high-performance computing, this feature enables photorealistic visualization on demand, making molecular structures clearer and more detailed than ever.

About VMD

For nearly three decades, Visual Molecular Dynamics (VMD) has been an essential tool for researchers in molecular modeling, structural biology, and computational biophysics. Originally developed in the mid-1990s, VMD was designed to provide a powerful, flexible, and scalable environment for visualizing and analyzing biomolecular structures. Today, with over 100,000 users worldwide, VMD has become a cornerstone of molecular dynamics research, enabling scientists to explore complex molecular interactions, study large-scale biomolecular assemblies, and gain critical insights into biological function.

One of the key reasons for VMD’s success is its versatility. Supporting a wide range of molecular file formats, VMD can handle systems from small molecules to massive molecular complexes with millions of atoms. It provides high-performance visualization tools, including advanced rendering techniques for publication-quality images and interactive analysis. Beyond visualization, VMD offers a comprehensive scripting environment through Tcl, allowing users to automate tasks, develop custom workflows, and extend its functionality to meet specific research needs. Combined with its tight integration with molecular dynamics software like NAMD, VMD has become an indispensable platform for simulating and analyzing the behavior of biomolecules at atomic resolution.

Another reason for VMD’s widespread adoption is its ability to extract all the modern computational power. Over the years, VMD has continuously evolved to leverage GPU acceleration, making it one of the fastest molecular visualization tools available. This has enabled real-time molecular rendering, large-scale trajectory analysis, and even the production of movies that are shown in planetariums all over the world, allowing researchers to process and visualize massive datasets with unprecedented efficiency. As computational biology has grown, so has VMD, ensuring that scientists always have access to state-of-the-art tools that push the boundaries of discovery.

VMD has long been the gold standard for molecular visualization, but VMD 2.0 brings a long-overdue improvement to its user interface, making it more intuitive and accessible than ever. Designed to streamline workflows and enhance usability, VMD 2.0 modernizes the visualization experience, helping users focus on their research rather than navigating complex menus. Additionally, this update ensures seamless compatibility with modern visualization hardware, including touchscreens and ultra-high-definition displays, allowing researchers to interact with their molecular systems in more immersive and efficient ways. By embracing cutting-edge rendering technologies and a more user-friendly design, VMD 2.0 makes molecular visualization more powerful, accessible, and future-ready.

About the TCBG

The Theoretical and Computational Biophysics Group (TCBG) at the University of Illinois at Urbana-Champaign (UIUC) is a world leader in computational biophysics, known for developing VMD (Visual Molecular Dynamics) and NAMD (Nanoscale Molecular Dynamics)—two of the most widely used tools in molecular modeling and simulation. Operating under the Beckman Institute for Advanced Science and Technology, TCBG was led by Professor Klaus Schulten until 2016 and is now directed by Professor Emad Tajkhorshid. The group pioneers advances in molecular dynamics, supercomputing, AI-driven analysis, and GPU acceleration, enabling breakthroughs in computational structural biology, large biomolecular complexes, membrane biology, and drug discovery. TCBG also plays a key role in scientific training and outreach, offering workshops that have trained thousands of researchers worldwide.

About Us

Disclaimer: Alpha Version in Development

VMD 2.0 is currently in its alpha release stage, and many features are still under active development. While this version introduces major improvements, including a new user interface, advanced rendering, and faster calculations, users should expect ongoing refinements and updates.

We are continuously working to enhance performance, stability, and feature completeness. Throughout 2025, we plan to release new versions every month, progressively refining the interface, plugins, and tools. This process will culminate in a final release, which will include a fully overhauled plugin system, improved usability, and expanded functionality.

We encourage users to explore VMD 2.0, provide feedback, and stay tuned for future updates as we shape the next generation of molecular visualization together.

A New Era in Molecular Visualization