Table of Contents

Molecular Simulations

The following exercises are part of the the course Molecular simulations held by Marcella Iannuzzi at the University of Zurich during the spring semester 2014.

Introduction

Getting familiar with the command line, Gnuplot and VMD.

  1. The bash terminal in MacOS X
  2. 2d plotting with Gnuplot
  3. 3d visualization with VMD
  4. Working on remote computers with SSH (optional)
Required files intro.tar

Week 1

Ingredients of a force field and molecular dynamics in action.

  1. Constructing a force field for the $\text{H}_2\text{O}$ molecule
  2. Molecular dynamics of liquid $\text{H}_2\text{O}$
Required files week1.tar

Week 2

Sampling dynamical properties, dealing with surfaces of crystals and a glimpse of QM/MM.

  1. Diffusion constant, viscosity and size effects
  2. QM/MM: Cyclohexaphenylene on Cu(111)
Required files week2.tar

Week 3

The 'chemical reaction' of $\text{NaCl}$ dissociating into $\text{Na}^+$ and $\text{Cl}^-$ in an aqueous environment and an example of a two-dimensional potential energy surface.

  1. Free and constrained molecular dynamics
  2. Profiles of potential energy and free energy
  3. Potential energy surface of Alanine dipeptide
Required files week3.tar