Program Overview

Introduction to Interactive Molecular Dynamics

The Interactive Molecular Dynamics simulation is a web-based application that models the behavior of simple atoms and molecules in a two-dimensional universe. This simulation is designed to explore phases of matter, emergent behavior, irreversibility, and thermal effects at the nanoscale.

The Physics Behind the Simulation

The simulation is based on the Lennard-Jones formula, which calculates the force between atoms as a function of their distance apart. The force is weakly attractive at short distances but strongly repulsive when the atoms touch. The simulation uses the Verlet algorithm to approximate Newton's laws of motion, with a natural system of units where the atomic diameter, atomic mass, depth of the Lennard-Jones potential, and Boltzmann's constant are all set equal to 1.

Simulation Parameters

• Number of atoms: 500
• Box size: 50 (volume = 2500) x10
• Gravity: 0.000
• Fixed Time step: 0.020
• Steps per frame: 25
• Atom color: Purple, Green, Yellow, Orange, Red, Magenta, Cyan, Blue, Forest, Black, White, Random, By speed
• Background: Black, White, Beige, Pink, Lavender, Sky, Sage, Navy, Plum, Brown, Gray

User Interface

The simulation can be controlled using various buttons and sliders, including:

• Start: starts the simulation
• Step: steps forward in time by a small amount
• Faster and Slower: increase and decrease the speeds of all atoms by 10%
• Freeze: sets all speeds to zero
• Reverse: runs the motion backwards (note: this is not always accurate due to chaotic motion)
• Box size: changes the width of the container and the scale of the image
• Statistics: displays time, total energy, temperature, and pressure

Additional Features

• Anchoring: allows users to artificially anchor one or more atoms in space
• Bonding: allows users to connect two atoms together with a spring-like force
• Fixing temperature: allows users to set the temperature of an atom, causing it to move randomly as if in contact with a heat bath
• Data collection: allows users to record various types of data, including system totals, selected atom, and all atoms

Technical Details

The simulation was created by Daniel V. Schroeder, Physics Department, Weber State University. It is computationally intensive, performing hundreds of basic computations per atom per time step. The simulation is available in version 1.0, last modified on August 6, 2014. Future versions will be posted, and the lack of standardization for touch-screen devices and browsers makes it difficult to improve support.