The Theoretical and Computational Biophysics Group is pleased to announce VMD version 1.9.1. 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 over 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 1.9.1 Documentation, Release Notes, Tutorials
  • Download VMD 1.9.1 for MacOS X, Unix, or Windows
  • VMD 1.9.1 Development and Release History (large)

    Major features included in VMD 1.9.1:

    Fast "QuickSurf" multi-resolution molecular surface
    calculation and display with CUDA GPU acceleration
    As reported in several publications, VMD uses GPUs to accelerate many of the most computationally demanding visualization and analysis features of interest to biomedical researchers. VMD 1.9.1 advances these capabilities further, adding a GPU-accelerated implementation of the new QuickSurf molecular surface representation, enabling smooth interactive animation of moderate sized biomolecular complexes consisting of a few hundred thousand to one million atoms, and interactive display of molecular surfaces for multi-million atom complexes, e.g. large virus capsids. The GPU-accelerated QuickSurf representation in VMD achieves performance orders of magnitude faster than the conventional Surf and MSMS representations, and makes VMD the first molecular visualization tool capable of achieving smooth animations of surface representations for systems of up to one million atoms. 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: molecular surface display 10x to 45x, 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.

    VMD molecular scenes with ambient occlusion lighting, shadows,
    and angle-modulated transparency, rendered with the
    Tachyon parallel ray tracer built-into VMD
    VMD 1.9.1 contains many features for generating high quality renderings of molecular graphics and for creation of movies of both static structures and molecular dynamics simulation trajectories. The updated 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 VMD Wavefront OBJ export feature has been extensively tested with the most recent versions of Autodesk's Maya, and 3ds-Max professional rendering tools. VMD also supports export to the RenderMan .rib file format used by Pixar's RenderMan, the open source renderer Aqsis, and many other animation and rendering tools.

    New Force Field Toolkit plugin assists with
    development of CHARMM-compatible parameters

    VMD remote control app for mobile
    Android phones and tablets
    The newly added NetworkView plugin provides a graphical interface for the study of allostery and signalling using network models, allowing networks to be mapped onto molecular structures loaded in VMD. The new Force Field Toolkit (FFTK) plugin provides tools that aid users in the development of CHARMM-compatible forcefield parameters, including charges, bonds, angles, and dihedrals. These tools are accessed through the provided GUI, which greatly simplifies the setup and analysis of the underlying calculations. Notable features include assisted generation of Gaussian input files and parsing of the resulting log files to obtain QM target data, access to downhill and simulated annealing optimization routines, and interactive fitting of dihedral parameters via embedded data plotting tools.
    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 significantly improves the display of large structures and long timescale trajectories.
    The newly added PropKa interface for graphical analysis of pH-dependent properties of proteins using the PROPKA package. The new NMWiz plugin provides a graphical interface for normal mode analysis. The RMSD Trajectory Tool has been updated with many new features including swapping of equivalent atoms, and calculation of average, std. deviation, and other useful statistics. The new RMSD Visualizer plugin allowed RMSD and RMSF values to be computed for specified atom selections and plotted using the new HeatMapper 3-D heat map generation tool and the Multiplot plugin.
    A new remote control feature of VMD 1.9.1 provides the ability to control a VMD session from mobile phones and wireless tablet devices. The remote control app allows mobile devices to manipulate the VMD molecular display, moving, rotating, and scaling the displayed molecular structure. Several user-defined remote control buttons can be used to trigger VMD scripts, drive presentations using an updated version of the ViewMaster plugin.

    MultiSeq analyzes large datasets efficiently
    This release of VMD includes the newly revised MultiSeq plugin. MultiSeq includes updated support for MAFFT for multiple sequence alignments. The latest version improves support for ClustalW and MAFFT alignments for sequences containing non-standard or unrecognized residues. Non-redundant set calculations can now be performed for a set of user-selected sequences. 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.