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Molecular Modeling ... a Cup of Joe?

© Adam Hughes

In the last few weeks, we've been building up our knowledge of object-oriented concepts, and we've seen that Java is causing quite a buzz for its unique characteristics. We have been able to apply what we've learned to develop a small conceptual model of what various chemistry-related objects might look like and how they might interact to make a useful simulation system. This week, we're going to start looking at how our hypothesizing meshes with what's going on in the real world of computer simulation. In particular, we're going to briefly survey the landscape of molecular dynamics (MD) applications written in Java.

One of the earliest Java-based molecular dynamics application was MDModel, developed at the University of Heidelberg for the "Software Praktikum" and first released in 1996. MDModel is different from most MD packages in that it doesn't strive for extreme accuracy in its calculations or for the simulation of millions of atoms. Rather, MDModel gives the user an interactive, one-molecule MD simulation session in which he can watch, instantaneously, how changes to various system parameters change the chemical species being studied.

The developers of MDModel also chose to take advantage of the presence of applets in the Java language, meaning the applet form of the program can be invoked from a web browser. While many MD programs have graphical user interfaces (GUIs) of some sort these days, not many are available through a browser. MDModel was also developed as a standalone Java application.

The graphical user interface of MDModel is where all of the good stuff happens for the computational chemist. The GUI consists of a 3D rendering area for showing the molecule being studied and lines of buttons and card-selectors to control the parameters of the system. Methods to control the rendering of the molecule and the running of the simulation include mouse-controlled translating, rotating, and scaling of the molecular image; buttons to control stopping and starting a simulations, as well as centering a molecule that "gets away"; and different "cards" to enter system information such as which kinds of forces to calculate, how to treat configuration data, and so on.

When changes are made to the above elements, the molecular display is updated, as well as any graphing of quantities that has been enabled. Such a hands-on simulation is quite different than what most of us in this segment of the computational world are used to. In fact, this type of interaction has led to the development of much of today's virtual reality products. The introduction of such technology to chemical modeling could be quite powerful in the years

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