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exercises:2015_uzh_molsim:index [2015/05/27 10:17]
yakutovich [Week 3 (tentative)]
exercises:2015_uzh_molsim:index [2020/08/21 10:15]
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-====== 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. 
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-===== Introduction ===== 
- 
-Getting familiar with the command line, Gnuplot and VMD. 
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-  - [[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 |}}| 
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-===== Week 1 ===== 
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-Ingredients of a force field and molecular dynamics in action. 
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-  - [[h2o_ff|Constructing a force field for the $\text{H}_2\text{O}$ molecule]] 
-  - [[h2o_md|Molecular dynamics of liquid $\text{H}_2\text{O}$]] 
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-|Required files | {{ week1.tar?direct&400 |}}| 
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-===== Week 2 ===== 
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-Sampling dynamical properties, dealing with surfaces of crystals and a glimpse of QM/MM. 
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-  - [[h2o_diff|Diffusion constant, viscosity and size effects]] 
-  - [[chp_cu111|QM/MM: Cyclohexaphenylene on Cu(111)]] 
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-|Required files | {{ week2.tar?direct&400 |}}| 
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-===== Week 3  ===== 
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-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. 
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-  - [[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]] 
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-|Required files | {{ week3.tar?direct&400 |}}| 
exercises/2015_uzh_molsim/index.txt ยท Last modified: 2020/08/21 10:15 (external edit)