Paper title: VMD: Visual Molecular Dynamics
Journal: Journal of Molecular Graphics (1996) (14, 33-38)

Author(s): William Humphrey, Andrew Dalke, and Klaus Schulten
*Theoretical Biophysics Group, University of Illinois and Beckman Institute, Urbana, Illinois 61801

Summary:
The paper introduces the capabilities, design and implementation of VMD or Visual Molecular Dynamics. It is a program that provides visualization of molecular dynamics simulations.
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The motivation of the authors for developing VMD is to provide researchers with a well-documented and freely available program that is easy to use and modify. It is written in C++ with an object-oriented design. It allows analysis of different molecular assemblies with a user-friendly interface.

Some features of VMD include the following:
- can simultaneously display many structures in 3-D using different rendering styles and colors
- acts as a visualization console for a separate MD application and can display the simulated molecule while its motion is being computed by the same MD application
- provides a complete graphical user interface for program control and a text interface for complex scripts with variable substitution, control loops and function calls
- has text- and mouse-based interface controls with user-customizable menu
- allows production of high-quality raster images f currently displayed molecular systems
- can also be rendered in stereo to enhance the appearance and information content of the displayed system
- may be paused anytime so that users may check on the progress of the simulation without having to restart everything

Molecules are read by the program through structure files and coordinate files. The first one contains molecular information such as bond connectivity, atomic mass and charge values. The latter contains the positions of the atoms that comprise the molecule. Atoms are displayed in VMD by using an extensive atom selection syntax that includes Boolean operators and regular expressions.

At the end of the paper, an example is given and details about the program’s documentation and availability are provided.

Contribution and application:

Although VMD has been initially developed for interactive display of biomolecular systems like proteins and lipids, it can easily be modified to meet the system demands of SWRO process simulations. By using it alongside NAMD, ESEL will have powerful tools for elucidating membrane fouling mechanism.



By: Hannah Ebro
hannah@gist.ac.kr