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Molecular Dynamics

Interactive Molecular Dynamic Simulation

For wider and better dissemination of scientific knowledge, AFR has made available here for free download and unlimited educational use its copyrighted proprietary Interactive Molecular Dynamic Simulation Software, an educational software tool for junior high, high school and college physics and chemistry students.

With one interface, the student (or teacher) adjusts the temperature of the physical system (via time of day or season) and sees the effect on molecules for different states of matter. With a separate interface, the student (or teacher) can adjust a number of parameters such as temperature; gravity; and the number, type and mass of atoms. The atoms can then be seen moving in 3-D space, and the student (teacher) can examine a chart of the resultant molecular energy and velocity.

System Requirements:

bulletOperating Systems: Windows 95/98/NT/NT2000
bulletMemory requirements: 16 MB for Windows 95, 32 MB for Windows 98, 64 MB for Windows NT and Windows 2000
bulletCPU: Pentium 166 MHz or higher
bulletHard drive space required: 20 MB
bulletVideo: 256-color SVGA or better (800x600 or higher)


This software is downloadable as two separate components:

1) Macroscopic Model (mdMacro.zip)

2) Statistical Mechanics Model (mdStatMech.zip)

To install the program, unzip the zip file and run the setup.exe.  To uninstall the software, run the Add/Remove programs from the Windows Control Panel.

Questions about the software can be emailed to: info@AFRinc.com (no phone calls please)

Macroscopic Module

The Macroscopic module is an interactive scene that allows students to explore the macroscopic world and to simultaneously view molecular dynamics at a microscopic level. The student is able to:

bulletPosition the sun by changing the time of day
bulletChange to the season to induce extended temperature excursions
bulletExplore various states of matter

With this module, the student is able to adjust the temperature of the system and see the effect on the molecules for different states of matter.

The states of matter which are simulated in the Macroscopic are:

Single component systems


Double component systems

bulletSolid / Gas
bulletSolid / Liquid
bulletLiquid / Gas

Statistical Mechanics Module

The Statistical Mechanics module is an advanced component of the Interactive Molecular Dynamics Simulation program. This module exposes all the parameters of the molecular dynamics model and gives the user ultimate flexibility to experiment with these parameters.

The following list of parameters may be adjusted:

bulletNumber of atoms
bulletNumber of types of atoms
bulletMass of atoms
bulletAtomic potential function

As the user adjusts these parameters they are able to see the effects. The results of the atoms moving in 3-D space are viewed in the main window. Additionally, the user may select various charts that show the Statistical Mechanics properties of the system. The following charts can be displayed by check the appropriate check box:

bulletHistograms representing Energy Distribution and Velocity Distribution
bulletStrip chart displaying Total Energy, Kinetic Energy, and Potential Energy
bulletPotential Function Graph/Editor

The Interactive Molecular Dynamics software was written and designed by Wayne Smith, Oskar Bosch, Jon Rifken, and Michael Serio. Contributions were also made by Sylvie Charpenay (the original author of the idea), Yonggang Chen, William Hamblen, David Hamblen, Eric Suuberg, David White, Luke Achenie and Tom Terry. We also wish to thank the users and evaluators whose suggestions have made it a much better program. Financial support of this work by the National Science Foundation under SBIR grant DMI-9860613 is gratefully acknowledged, along with the support and encouragement of Dr. Sara Nerlove, the NSF project officer.

Additional related work by Jon Rifkin can be found at the website for The Center for Materials Simulation at the University of Connecticut AtomDemo:



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For More Information Contact:
Advanced Fuel Research, Inc.
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Tel: 860-528-9806
Fax: 860-528-0648

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Last modified V3: September 18, 2009