VMD 1.8.3 - A small step in version number, a big step in science features

The Theoretical and Computational Biophysics Group is pleased to announce VMD version 1.8.3. Despite the inconspicuously small increase in version number, the latest VMD offers powerful new features that will greatly benefit life scientists and attract many new researchers to the ranks of the VMD user community.

VMD 1.8.3
VMD 1.8.3 Screen Shot

Major features included in VMD 1.8.3:

VMD includes a new multiple alignment plugin which can align structures and sequences of multiple proteins, color the proteins according to structure or sequence similarity and show conserved residues. The alignment algorithm underlying this feature is STAMP developed by R.B. Russell and G.J. Barton. The multiple alignment plugin, available in the VMD extension menu, has been developed by the group of Professor Zan Luthey-Schulten, Professor of Chemistry at UIUC, who joined the VMD development team.

VMD users have long demanded an improved secondary structure or "cartoon" representation. VMD 1.8.3 offers a highly accurate and yet simple secondary structure representation that furnishes beautiful publication quality images, while retaining the speed of the original "cartoon" representation.

With the increasing size of structurally resolved biomolecular systems explored through molecular modeling, users routinely analyze multi-gigabyte molecular dynamics trajectories. VMD 1.8.3 adds support for AMD64 and EM64T processors from AMD and Intel, 64-bit processors that permit addressing huge data sets that essentially abolish trajectory size limitations for VMD. With this addition, VMD supports all of the mainstream 64-bit graphics workstations.

VMD can now calculate, just as its sister program NAMD does, electrostatics based on the Particle-Mesh-Ewald (PME) algorithm. The new PME potential plugin allows users to calculate readily electrostatic potential energy maps averaged over trajectories. A first application to the membrane protein hemolysin can be found in this paper

VMD has become popular in lectures and even in the class room. While some lecturers' virtuosity in VMD use is so great that they execute VMD commands live, others prefer to prepare views in advance and show them with the click of a button. Such views can easily be prepared and displayed using the new ViewMaster plugin.

Short list of other popular features and improvements in VMD 1.8.3:

  • Initial support for OpenGL shading language (GLSL) for very high quality shading of interactive molecular graphics.
  • Easy-to-use graphical interface for the Solvate plugin
  • New Intersurf plugin for drawing interaction surfaces between groups of atoms.
  • New "Volume" coloring method, for use with electrostatic potential maps, and other volumetric datasets. Requires OpenGL 1.2 3-D texture mapping.
  • New "measure sasa" command to measure solvent accessible surface area for an atom selection.
  • New Camera Navigator plugin allows the user to fly the camera using the keyboard in perspective projection mode.
  • New Clipping Plane plugin provides a simple interface to manipulate the 6 user-defined clipping planes to one, all active, or all molecules.
  • 17 new or improved file reader plugins provide support various structure and trajectory formats, and greatly improved I/O performance for large trajectories.
  • Significantly improved Tachyon and POV-Ray output for MSMS surfaces, NewRibbons, and other triangulated surface geometry.
  • The vmdmovie plugin now generates movies much more quickly, and supports the use of POV-Ray for ray tracing of movies