VMD is a software application that was designed to allow biophysics and chemistry specialists to visualize, analyze and animate molecules and molecular systems in 3D mode.
The application offers a complex set of functions that users can take advantage of to study both simple and complex molecular scenes. After the installation is complete, the tool will display three separate windows: an information window, a display window and a menu window. The first window keeps track of the actions taken by the user while working with this tool, the second window displays the molecular systems imported by the user, while the third one gives access to all the functions of the tool.
Mention should be made of the fact that this program does not provide default databases containing molecular data files. In order to visualize a molecule or a molecular system, users need to import their own databases containing 3D representations of molecules.
Users can then visualize them by accessing the "File" section from the main menu and select the "New molecule" inlay. A new window will allow them to import the file they wish to open. Once the molecule or molecular system is shown on the display window, the users will be able to view its different components, to manipulate it using the Graphical Representations panel, and even create viewpoints and representations.
Various options are available for the display window as well. Therefore, users can change the background color of the display so that the contrast with the molecular system allows them to visualize its components in a better way. They can also divide the screen into two parts so that they can view different sections of the same molecule at the same time.
The "Extensions" section allows users to perform different analyses on the molecular systems, while the Modeling subsection allows them to add different components to the system.
All in all, VMD is an extremely useful tool for biophysics and chemistry specialists, as well as for other scientists who are undertaking research in the field. The different functions of the program can be easily handled to get the best results for the automatic simulation, analysis and animation of 3D molecular systems.
v1.9 [Feb 27, 2011]
README: added a note regarding the crdplugin update
viewchangerender: Corrected display of total movie duration.
vmdmovie: Force numframes to be an int.
timeline: tweaked control placement to look good on Mac, Windows, and Linux
Added extra calls to FLTK size_range() method to try and workaround what appears to be an FLTK bug on MacOS X where the OpenGL window can become non-resizable under certain conditions.
crdplugin: Cranked minor version of CRD plugin due to recent change to box output formatting.
crdplugin: Fixed formatting of AMBER CRD box info when writing CRD files.
Added extra safety checks on remaining minmaxlist[] accesses in the GUI callbacks.
Free any remaining tubearray at shutdown.
Fix a tiny leak that could occur if no QM orbitals are loaded by an Orbital rep gets created/updated.
Added initialization of orbital rep variables that turned up in a valgrind test run.
Fix unprotected accesses to the minmaxlist used to define the active range for isovalue sliders. The GUI code now sets the minmax range to 0:1 if there are no valid volumetric datasets loaded.
Set default state of the cullingEnabled member variable in the DisplayDevice base class constructor, curing an uninitialized reference in the OpenGL subclasses, found by valgrind.
Fix a single string that was being leaked in the FileRenderer destructor found with valgrind.
Updated the X3D export code, creating a new subclass that implements export for X3DOM version 1.1, which can only handle a subset of the X3D scene nodes possible in the full specification. As X3DOM implements more X3D nodes in future versions, we can remove virtual method overrides until X3DOM can handle everything that the full X3D export subclass uses. The X3DOM-specific export shows up in the Render window GUI as second X3D option, and the script renderer name is "X3DOM".
README: Added note about expanded range of label format specifiers
And more...
