VMD 1.9

The Theoretical and Computational Biophysics Group is pleased to announce VMD version 1.9. VMD incorporates many new improvements for high quality rendering and export of molecular scenes, new analysis features, support for new molecular data file formats, and many performance improvements. Many new and updated structure building and analysis tools have been added in this release, easing the process of preparing, running, and analyzing biomolecular simulations. This release also contains many performance and efficiency improvements that are particiularly beneficial for modeling, visualizing, and analyzing very large structures with up to 100 million atoms. VMD makes extensive use of multi-core processors and GPU acceleration to speed up computationally demanding analysis and visualization tasks including key structure and trajectory analysis features, interactive molecular dynamics, and high-quality ray tracing of molecular scenes. VMD now takes advantage of multiple GPUs for very fast display of molecular orbitals arising in quantum chemistry calculations.

  • VMD 1.9 Documentation, Release Notes, Tutorials
  • Download VMD 1.9 for MacOS X, Unix, or Windows
  • VMD 1.9 Development and Release History (large)

    Major features included in VMD 1.9:


    VMD/Tachyon renderings with
    ambient occlusion lighting

    VMD molecular scenes with ambient
    occlusion lighting, shadows, and
    angle-modulated transparency, rendered
    with the Tachyon parallel ray tracer
    built-into VMD

    Angle-modulated transparency in VMD:
    OpenGL (left), Tachyon (right)

    VMD 1.9 exports large models to Wavefront OBJ
    format much more efficiently, enabling professional
    animation tools like Maya to easily incorporate
    molecular graphics from VMD
    VMD 1.9 contains many new and improved features for generating high quality renderings of molecular graphics and for creation of movies of both static structures and molecular dynamics simulation trajectories.
    The molecular graphics export features of VMD have been significantly enhanced in the latest version. The built-in Tachyon parallel ray tracer in VMD has been improved with faster rendering, and it now supports all of the special VMD rendering and shading features including angle-modulated tranparency, all depth cueing modes, and background gradients.
    VMD now supports the X3D scene format, which can be used to make documents with interactive embedded 3-D molecular graphics. The latest WebGL-capable web browsers can interactively display VMD molecular graphics in X3D format, without the need for any additional browser plugins.
    The VMD export modules for Raster3D, RenderMan, POV-Ray, Tachyon, VRML2/VRML97, and X3D have been udpated to add full support for text rendering, e.g. atom labels, angles, bond lengths, time-varying distance measurement labels, and user-defined text, enabling text labels to be shown in high-quality ray traced renderings and movies.
    VMD now exports large models to the Wavefront OBJ scene format with much greater efficiency. VMD now exports material properties, molecular representation groupings, and exports molecular geometry in a more efficient way, resulting in much smaller scene files that are easier for other programs to work with. The Wavefront OBJ file format supported by many commercial rendering and animation packages, and with these improvements professional visualization artists can more easily incorporate molecular graphics directly from VMD into their rendering tools. The improved Wavefront OBJ export feature has been extensively tested with the most recent versions of Autodesk Maya, and the embedded VMD representation "grouping" information makes it easier to work with imported VMD scenes within the Maya graphical interfaces.
    The VMD movie maker plugin has been updated to support a broader range of rendering and movie compression formats and options. The new ViewChangeRender plugin provides an easy-to-use graphical interface for managing multiple VMD camera viewpoints and making movies that fly the camera between multiple viewpoints.
    The new version of VMD adds support for a broader range of stereoscopic display hardware, including displays that use "checkerboard" and column-interleaved formats used by DLP HDTVs and projectors, and the column-interleaved format used by autostereoscopic displays. The anaglyph (red/cyan) stereo mode has been adapted to support inexpensive gaming GPUs and laptop graphics chipsets. New graphical menus make it easy to swap the left and right eyes in all supported stereo modes, for hardware configurations that reverse the eyes, and to simplify the creation of cross-eye and wall-eye stereo images.


    Faster multi-GPU molecular orbital
    calculation and display with CUDA
    VMD 1.9 further advances the use of GPU accelerated molecular visualization and analysis, based on NVIDIA CUDA, and most recently adding support for OpenCL (use of OpenCL requires compilation from source code at present). As reported in several publications, the massively parallel architecture of GPUs makes them ideal devices to accelerate many of the computationally demanding calculations in VMD. The range of acceleration provided by GPUs depends on the capabilities of the specific GPU device(s) installed, and the details of the calculation. Typical acceleration factors for the algorithms in VMD on a single high-end GPU are: electrostatics 22x to 44x, implicit ligand sampling 20x to 30x, calculation of radial distribution functions 30x to 90x, molecular orbital calculation 100x to 120x. Details on making best use of the GPU acceleration capabilities in VMD are provided here.


    Structure building with Molefacture

    Carbon nanostructures built with VMD
    VMD 1.9 incorporates many improvements aimed at increasing its structure building capabilities. The latest version of the molefacture plugin performs geometry optimisations and can assign charges using the latest versions of SQM and antechamer (distributed with ambertools). Molefacture now allows structures to be built for the OPLS force field, based on included CHARMM-formatted OPLS parameter files. Molefacture also provides an FEP setup tool to aid in the generation of structures and input files for free energy perturbations with NAMD.
    VMD reads, stores, and writes angles, dihedrals, impropers, and cross-term maps, and includes text commands for querying and setting these fields enabling the development of flexible structure building tools such as the new topotools plugin. The toptools plugin makes it much easier to develop customized structure building tools like the newly updated Carbon Nanostructure Builder plugin.
    The new Chirality, and Cispeptide plugins help researchers build their structures, by detecting, visualizing, and correcting, and enforcing chirality and peptide bond configuration in proteins. A new tutorial describing the Cispeptide and Chirality plugins is available here. The new MDFF plugin provides commands for fitting atomic structures to a density map, using the molecular dynamics flexible fitting method.

    Trajectory analysis with Timeline
    VMD 1.9 also includes several new molecular dynamics analysis features. The new ParseFEP plugin provides a set of tools for analyzing free-energy perturbation (FEP) calculations performed with NAMD. The PLUMED plugin allows collective variable analysis from within VMD, using PLUMED. VMD includes a new GPU-accelerated method for computing radial distribution functions up to 90x faster than with the CPU alone, and a new version of the graphical g(r) plugin includes support for the GPU-accelerated calculations.
    The updated Timeline plugin provides an interface for viewing temporally changing per-residue attributes of a molecular structure. It can also display temporally changing attributes of a set of VMD selections, for example a set of all the salt-bridge pairs observed in a trajectory. The controls allow selection of the molecule, or part of the molecule, used for the calculation. The graphical display of residues and timesteps can be scrolled and zoomed as necessary to see results for large structures and long trajectories. The latest version improves performance for large structures and long trajectories, provides more analysis functions and options, and significantly improves the printing features for saving Timeline trajectory analysis plots as encapsulated Postscript (.eps) files.

    MultiSeq analyzes large datasets efficiently
    This release of VMD includes the newly revised MultiSeq plugin version 3.1. MultiSeq has added new support for MAFFT for multiple sequence alignments. RMSD and Q calculations now work for RNA as well as DNA. The title shown for a sequence can now be changed from simply 'Sequence Name' to a variety of options including Scientific Name, Common Name, Domain of Life, and many others. Major efforts have been directed toward improving the ability of MultiSeq to handle large data sets, and the new MultiSeq is capable of loading and analyzing 100,000 sequences on a typical desktop machine.