**Interactive Demonstrations**

Topic | Run Demonstration | Description |
---|---|---|

Interactions | Description | |

Nonbond Cutoffs | Description | |

Periodic Boundary Conditions | Description | |

Molecular Dynamics | Description | |

Maxwell-Boltzmann Distribution of Velocities | Description | |

Velocity Scaling and Equilibration | Description | |

Minimization | Description |

1.

- Illustrates the intramolecular bonding and nonbonding interactions used in molecular

mechanical forcefields:

- Bond deformation: quadratic

- Bond deformation: Morse

- Bond angle deformation: quadratic

- Torsion angle deformation

- Out-of-plane deformation

- Lennard-Jones London-van der Waals

- Electrostatic Coulombic

- Bond deformation: quadratic
- 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:

- Hard spherical cutoff (discontinuous energy and force)

- Shifted potential (continuous energy, discontinuous force)

- Shifted force (continuous energy and force)

- Switching function (continuous energy and force)

- Hard spherical cutoff (discontinuous 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:

- Generate random numbers according to a normal distribution

- Scale these random numbers to generate velocities according to a Maxwell-
Boltzmann distribution for the specified temperature

- Generate random numbers according to a normal distribution
- 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.

- 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.