VMD

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.