JCE Software, 1D1: Molecular Dynamics Simulator

DYNAM: Molecular Dynamics Simulator

G. Peter Matthews
Polytechnic South West, Plymouth, England
Emerson F. Heald
Thiel College, Greenville, PA 16125

Note:
This program is included in the Advanced Chemistry Collection (SP-28).

To Order Advanced Chemistry Collection

Molecular Dynamics Simulator provides a display of molecular motion in a solid, liquid, or gas. An updated version of the program described by Matthews (1), it shows nonpolar molecules moving under the influence of the Lennard-Jones 6-12 potential function.

Screen from the Molecular Dynamics Simulator.
Initially, a small sample of 32 molecules is placed in a cubic lattice. The molecules are assigned random velocities and inhabit a cubic section of three-dimensional space which repeats itself over and over in each direction. A periodic boundary condition applies if a molecule leaves through the one side of the cube, it appears on the opposite side. The molecules interacting with a given molecule are its closest neighbors, including ones in neighboring cubes.
The user supplies values of the temperature and number density, or number of molecules per unit volume. One of three things happens as the calculation proceeds:

At low temperatures and high densities, the molecules are so close to one another that they remain in the solid structure. The molecules move around their equilibrium positions in the lattice, but they cannot move past one another.

At high temperatures and low densities, the molecules are far enough apart that intermolecular forces are negligible. In this case they move in straight lines. If two molecules approach, they are first attracted and then repelled, simulating a collision. After a while all memory of the original solid is lost and the molecules behave as if they are in a gas.

At intermediate temperatures and densities, the molecules are far enough apart to be able to move past each other but close enough that they are continually attracted and repelled by each other. In this case the molecules move in random curved trajectories and their behavior simulates that of a liquid.
The sample of molecules is too small to simulate the behavior of a multiphase system, but users can clearly see how molecular motion differs in solid, liquid, and gas states.
The display provided by the program is a view of the cube from one side. Molecular motion can be observed either as tracks (lines tracing the position of the centers of the molecules) showing where the molecules have been or as spheres (circles) having the collision diameters of the molecules. The spheres move and leave shadows showing where they have been.
Hardware and Software Requirements
Series D of JCE: Software requires Microsoft Windows version 3.0 or later and associated hardware as defined by Microsoft. We recommend an IBM-PC/AT, PS/2, or compatible computer with a 80386 or higher processor, a minimum of 4 MB of memory, a hard disk, one floppy disk drive to install the software, and a Windows-compatible graphics card, such as an IBM VGA or a Super VGA adapter with a compatible color monitor, and a mouse. DOS version 5.0 or later is highly recommended.
In addition to the hardware and software recommended above, Molecular Dynamics Simulator benefits greatly from the presence of a math coprocessor, which is highly recommended.
Literature Cited

Matthews, G. P. Experimental Physical Chemistry; New York: Oxford University Press, 1985; pp. 336-349.

First Published: June 1993
Citation: Matthews, G. P.; Heald, E. F. . DYNAM: Molecular Dynamics Simulator J. Chem. Educ. Software 1D1
Keywords: Lecture Aid; General; Physical; Molecular motion

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Last Updated: July 19, 2001
Created: December 4, 1996 Created by: J. L. Holmes
Comments to: jceonline@chem.wisc.edu

© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.



DYNAM: Molecular Dynamics Simulator
G. Peter Matthews Polytechnic South West, Plymouth, England Emerson F. Heald Thiel College, Greenville, PA 16125

Note:	This program is included in the Advanced Chemistry Collection (SP-28). To Order Advanced Chemistry Collection

Molecular Dynamics Simulator provides a display of molecular motion in a solid, liquid, or gas. An updated version of the program described by Matthews (1), it shows nonpolar molecules moving under the influence of the Lennard-Jones 6-12 potential function. Screen from the Molecular Dynamics Simulator. Initially, a small sample of 32 molecules is placed in a cubic lattice. The molecules are assigned random velocities and inhabit a cubic section of three-dimensional space which repeats itself over and over in each direction. A periodic boundary condition applies if a molecule leaves through the one side of the cube, it appears on the opposite side. The molecules interacting with a given molecule are its closest neighbors, including ones in neighboring cubes. The user supplies values of the temperature and number density, or number of molecules per unit volume. One of three things happens as the calculation proceeds: At low temperatures and high densities, the molecules are so close to one another that they remain in the solid structure. The molecules move around their equilibrium positions in the lattice, but they cannot move past one another. At high temperatures and low densities, the molecules are far enough apart that intermolecular forces are negligible. In this case they move in straight lines. If two molecules approach, they are first attracted and then repelled, simulating a collision. After a while all memory of the original solid is lost and the molecules behave as if they are in a gas. At intermediate temperatures and densities, the molecules are far enough apart to be able to move past each other but close enough that they are continually attracted and repelled by each other. In this case the molecules move in random curved trajectories and their behavior simulates that of a liquid. The sample of molecules is too small to simulate the behavior of a multiphase system, but users can clearly see how molecular motion differs in solid, liquid, and gas states. The display provided by the program is a view of the cube from one side. Molecular motion can be observed either as tracks (lines tracing the position of the centers of the molecules) showing where the molecules have been or as spheres (circles) having the collision diameters of the molecules. The spheres move and leave shadows showing where they have been. Hardware and Software Requirements Series D of JCE: Software requires Microsoft Windows version 3.0 or later and associated hardware as defined by Microsoft. We recommend an IBM-PC/AT, PS/2, or compatible computer with a 80386 or higher processor, a minimum of 4 MB of memory, a hard disk, one floppy disk drive to install the software, and a Windows-compatible graphics card, such as an IBM VGA or a Super VGA adapter with a compatible color monitor, and a mouse. DOS version 5.0 or later is highly recommended. In addition to the hardware and software recommended above, Molecular Dynamics Simulator benefits greatly from the presence of a math coprocessor, which is highly recommended. Literature Cited Matthews, G. P. Experimental Physical Chemistry; New York: Oxford University Press, 1985; pp. 336-349.


News \| Issues \| CD-ROM / Video \| Find It! \| Technical Support \| For Authors
JCE Online \| Journal \| Software \| Internet \| Happenings \| About JCE \| Contact JCE

Last Updated: July 19, 2001 Created: December 4, 1996	Created by: J. L. Holmes Comments to: jceonline@chem.wisc.edu

© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.