VMD Plugin Library

VMD 1.8.5 Plugin Update 1, Released 11/15/2006

This is the first plugin update for VMD 1.8.5. The release includes new and improved molecule file reader/writer plugins, as well as improvements to several of the GUI extension plugins included with VMD 1.8.5.

New features and improvements in this plugin release:

  • BioCoRE chat plugin: misc user interface improvements
  • cgtools: new graphical user interface for coarse graining plugin
  • molefacture: numerous bug fixes, scalability, and performance improvements
  • multiplot: automatic color cycling, improved predefined colors, allow drawing of arbitrary items into the multiplot Tk canvas.
  • Add multiplot legends to exported xmgrace plot files. (Jerome Henin's patch)
  • paratool: many small bug fixes and improvements
  • psfgen: Extend PSF_RECORD_LENGTH to not cut off long file names in remarks.
  • qmtool: many small bug fixes and improvements
  • solvate: will automatically switch to a hexadecimal segname generation scheme when too many segments would be created for the max segname string length. Solvate now calls resetpsf to free memory prior to loading the newly created water box, in order to save memory. timeline: applied Charles McCallum's patch to improve the match between timeline secondary structure coloring and the VMD structure representation change color of 3_10 helices to blue as suggested by Charles Mccallum (and synced with new timeline plugin coloring)

New and improved molfile plugins

  • BRIX plugin now recognizes ".brx" extensions as well.
  • New CHARMM PBEQ potential map reader plugin
  • Updated CHARMM 31 expanded format PSF reading code to correctly read the atom type field.
  • Added support for reading and writing binary DX files. (Justin Gullingsrud's patch)
  • Improve the behavior of atom assignment in the LAMMPS dump reader plugin. (Lutz Maibaum's patch)
  • Prevent long segment names from overflowing the PDB segname field. (Axel Kohlmeyer's patch)
  • Add CRYST1 parsing to the PQR plugin. (Axel Kohlmeyer's patch)
  • Added support for reading binary UHBD grids. (Justin Gullingsrud's patch)
  • VASP potcar/poscar/chgcar plugins improvements to add "spin up" and "spin down" volume sets. Fix reading potcar files. (Rob Lahaye's patch)
  • XYZ plugin now exports atomic element data when available (Axel Kohlmeyer's patch)

Installing the new plugins:

The link below will download the latest directory of VMD 1.8.5 compatible plugins for all of the supported platforms. We intend to provide a new "updater" plugin soon. Until the updater plugin is ready, you may manually unpack this plugin distribution into a directory on your system. Once unpacked, you can use the new plugins either by replacing the plugin directory in your installed VMD distribution, or by adding commands similar to the following examples, to your personal .vmdrc or vmd.rc file. In order to utilized updated GUI extensions, you must replace the plugins in your installed VMD distribution. If you only want updated molecule file plugins, the .vmdrc/vmd.rc based plugin update method is sufficient.

Unix and MacOS X .vmdrc additions: 

menu main on
# Load the molecule file reader plugins from ~/plugins/....
# This command will evaluate to something like:
#   vmd_plugin_scandirectory   /users/johns/plugins/SOLARIS2/molfile   *.so
vmd_plugin_scandirectory [file join $env(HOME) plugins [vmdinfo arch] molfile] *.so

Windows vmd.rc additions: 
menu main on
# Load the molecule file reader plugins from c:/plugins
vmd_plugin_scandirectory   c:/plugins/WIN32/molfile   *.so

Newest VMD 1.8.5 plugins for all platforms

Note that when unpacked, this archive will consume approximately 70MB of disk space. Once unpacked, you may delete the subdirectories which correspond to architectures you don't need or use.

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