VMD 1.9.1The 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 accelerationVMD molecular scenes with ambient occlusion lighting, shadows,
and angle-modulated transparency, rendered with the
Tachyon parallel ray tracer built-into VMDNew Force Field Toolkit plugin assists with
development of CHARMM-compatible parameters
VMD remote control app for mobile
Android phones and tablets
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 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.