====== Molecular Simulations ======

The following exercises are part of the the course [[http://www.vorlesungen.uzh.ch/FS15/suche/sm-50018861.modveranst.html|Molecular simulations]] held by [[http://www.pci.uzh.ch/iannuzzi/|Marcella Iannuzzi]] at the University of Zurich during the spring semester 2015.

===== Introduction =====

Getting familiar with the command line, Gnuplot and VMD.

  - [[ssh|Working on remote computers with SSH (Linux, MacOS X, Linux)]]
  - [[bash_terminal|The bash terminal]]
  - [[gnuplot|2d plotting with Gnuplot]]
  - [[vmd|3d visualization with VMD]]
  - [[cp2k|Running a simple example with CP2K]]
 
|Required files | {{ intro.tar?direct&400 |}}|

===== Week 1 =====

Ingredients of a force field and molecular dynamics in action.

  - [[h2o_ff|Constructing a force field for the $\text{H}_2\text{O}$ molecule]]
  - [[h2o_md|Molecular dynamics of liquid $\text{H}_2\text{O}$]]

|Required files | {{ week1.tar?direct&400 |}}|

===== Week 2 =====

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

  - [[h2o_diff|Diffusion constant, viscosity and size effects]]
  - [[chp_cu111|QM/MM: Cyclohexaphenylene on Cu(111)]]

|Required files | {{ week2.tar?direct&400 |}}|

===== 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.

  - [[nacl_md|Free and constrained molecular dynamics]]
  - [[nacl_free_energy|Profiles of potential energy and free energy]]
  - [[alanine_dipeptide|Potential energy surface of Alanine dipeptide]]

|Required files | {{ week3.tar?direct&400 |}}|