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More on Java-Based Molecular Dynamics

© Adam Hughes

Our survey of Java-based molecular dynamics software takes us this week to Boston University's (BU) Center for Polymer Studies. As one might expect from the name of the institution, polymer studies are the order of the day. As with many polymer projects, modeling at BU is becoming an ever more important piece of the research puzzle. In this particular case, scientists are also taking advantage of the features of Java to create the best tools possible.

The Virtual Molecular Dynamics Laboratory is a suite of research-grade codes that serve as molecular dynamics (MD) tools and curriculum guides. Among these tools are several Java applets, aimed specifically at helping the researcher visualize salient features of a chemical system. Specifically, these include applets for running Lennard-Jones simulations, for examining interactions between two particles, for generating movies of molecular interactions, and for examining a new type of self-avoiding random walk simulation.

The Lennard-Jones applet gives the user control over a wide range of system properties, including temperature, density, pressure, number of particles, and particle mass, among other quantities. The type of boundary conditions to be used can also be varied, as can the Lennard-Jones interaction parameters, the type of box in which the simulation is run, and even the color of the particles! Having set up the system as desired, the researcher can then watch the dynamics simulation run to see what happens to the system with the evolution of time.

The Intermolecular Interaction applet allows the researcher to study closely the interaction between two particles. The user can choose the interactions parameters to be used, the velocity with which each particle is moving, and the mass of each particle. Then, he can see graphs of the interaction energy vs. time or vs. distance between the particles. Such graphs often yield important information into the nature of bonding and other chemical phenomena.

The Movie applet allows the user to play an animation of multiple particle interactions generated from a square-well potential. the movie can be played forward or backward, shifted up, down, left, and right, or stopped for closer examination. This can be quite valuable when trying to gain insight into some dynamic process, such as diffusion.

Finally, the Polymer applet allows the researcher to investigate a system utilizing the Infinitely Growing Self-Avoiding Walk (IGSAW). The walks can theoretically grow infinitely long and can thus be used to study quite large polymer systems.

Overall, the software developed at the Center for Polymer Studies is quite impressive and offers a good overview of what can be accomplished in combining Java technology with molecular dynamics techniques. For a closer look, visit their web site at

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