Molecular Dynamics
A simple Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. This is a reasonably accurate model of then interactions between noble gas atoms.  The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small time steps dt, the system's total energy should be approximately conserved.
References:
The Molecular Dynamics model is based on a Java applet written by Dan Schroeder, Physics Department, Weber State University.  See:
This simulation was created by Wolfgang Christian using the Easy Java Simulations (Ejs) modeling tool and is designed to teach modeling.  Users can inspect and modify the underlying model by copying the model from the running program into Ejs.  Right click within the simulation to examine the model in Ejs. 
You can examine and modify this simulation if you have Ejs installed by right-clicking within a plot and selecting "Open Ejs Model" from the pop-up menu. Information about Ejs is available at: .
The Easy Java Simulations (EJS) manual can be downloaded from the ComPADRE Open Source Physics collection and from the Ejs website.
See:
"Modeling Physics with Easy Java Simulations" by Wolfgang Christian and Francisco Esquembre, The Physics Teacher, November 2007, 45 (8), pp. 475-480.

Molecular Dynamics Physics
Dan Schroeder describes the physics of the Lennard-Jones molecular dynamics model as follows:
The force between the molecules is calculated from the Lennard-Jones formula (truncated at a distance of 3 molecular diameters). This is a reasonably accurate model of the interactions between noble gas atoms.

The model uses a natural system of units, with the molecular diameter, the molecular mass, the depth of the Lennard-Jones potential, and Boltzmann's constant all set equal to 1. For argon (for example), the unit of distance is 3.4 angstroms, the unit of mass is 40 atomic mass units, and the unit of energy is 0.01 electron-volts; the corresponding unit of time is then 2.2 picoseconds, the unit of velocity is 160 meters per second, and the unit of temperature is 120 kelvin.

The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt, the system's total energy should be approximately conserved.

The walls exert a linear (spring) force on the molecules, with a spring constant of 50 in natural units.

There's also an optional uniform downward force, controlled by the the gravity parameter. The magnitude of this force, however, is not meant to be realistic. Earth's gravitational constant is utterly negligible in the units used here (a little over 10-13 for argon).

That's all the physics! Everything else you see is a consequence of these basic laws (applied repeatedly as the molecules move), plus the initial placement of the molecules. The simulation code knows nothing about phase transformations or crystal structure or irreversibility.
References:
The Molecular Dynamics model is based on a Java applet written by Dan Schroeder, Physics Department, Weber State University.  See:

[color=blue][b]Wonderful work on the jar upload !![/b][/color]


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