• Illustrates the intramolecular bonding and nonbonding interactions used in molecular
  mechanical forcefields:
  
  1. Bond deformation: quadratic
     
  2. Bond deformation: Morse
     
  3. Bond angle deformation: quadratic
     
  4. Torsion angle deformation
     
  5. Out-of-plane deformation
     
  6. Lennard-Jones London-van der Waals
     
  7. Electrostatic Coulombic
     
• Plots the energy as a function of the relevant coordinate.
  
• Allows the user to alter the values of the parameters and compare plots.
  

• Illustrates four different approaches for applying cutoffs to nonbond interactions:
  
  1. Hard spherical cutoff (discontinuous energy and force)
     
  2. Shifted potential (continuous energy, discontinuous force)
     
  3. Shifted force (continuous energy and force)
     
  4. Switching function (continuous energy and force)
     
• Plots the energy and force as a function of distance between 2 particles interacting
  according to a Lennard-Jones potential.
  

• Illustrates the concept of periodic boundary conditions in 2-dimensions.
  
• Allows the user to move the particles in the central box to see ghost or image particles move with the particle in the central box.
  
• Allows the user to apply cutoffs (both minimum image and explicit image) to
  determine the included interactions for each particle in the central box.
  

• Illustrates energy conservation and time-reversibility for molecular dynamics.
• Illustrates the relation between time step, mass, and velocities for molecular dynamics.
  
• Performs molecular dynamics for 2 particles moving in 1-dimension according to
  a Lennard-Jones potential.
  
• Plots the kinetic, potential, and total energies as a function of time.
  
• Allows the user to reverse the velocities at any time to study time-reversibility.
  
• Allows the user to alter the values of the initial velocities and positions, the masses, and the time step to study the effects on energy conservation and time-reversibility.
  

5. Maxwell-Boltzmann Distribution of Velocities

• Illustrates the Maxwell-Boltzmann distribution of velocities and speeds for a specified
  temperature.
  
• Illustrates the method by which velocities are initialized to a Maxwell-Boltzmann
  distribution for a molecular dynamics simulation:
  
  1. Generate random numbers according to a normal distribution
     
  2. Scale these random numbers to generate velocities according to a Maxwell- Boltzmann distribution for the specified temperature
     
• Plots the resulting distributions of the 3 components and magnitudes of the intial velocities
  
• Allows the user to alter the temperature to compare the Maxwell-Boltzmann distributions.
  

• Illustrates the use of velocity scaling for equilibration during molecular dynamics.
  
• Performs molecular dynamics for a system of particles interacting according to a
  Lennard-Jones potential with periodic boundary conditions.
  
• Scales the velocities to the target temperature of 300 K every 500 time steps.
  
• Plots the kinetic, potential, and total energies as a function of time.
  
• Allows the user to plot 500 steps at a time to see the effects of velocity scaling.
  

7. Minimization

• Illustrates the steepest descents and simulated annealing minimization methods.
  
• Illustrates the concept of getting trapped in local minima.
  
• Illustrates the dependence of simulated annealing on the initial temperature and on the rate of cooling.
  
• Performs minimizations for a particle moving on a 1-dimensional potential surface with three minima of different energies.
  
• Allows the user to place the particle anywhere on the 1-dimensional potential surface prior to minimization.
  
• Allows the user to alter the initial velocity and the velocity damping factor
  for the simulated annealing minimization.