CP2K Open Source Molecular Dynamics

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exercises:2014_uzh_molsim:h2o_md

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exercise:mm_uzh:h2o_md [2014/05/02 17:20] – talirzexercises:2014_uzh_molsim:h2o_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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   * Check that the MD is energy conserving and //well-behaved//.    * Check that the MD is energy conserving and //well-behaved//. 
-  * FIXME additional question 
 </note> </note>
  
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 </note> </note>
  
-Now we are going to analyze the trajectories in order to calculate the [[http://en.wikipedia.org/wiki/Radial_distribution_function|radial distribution function]] (rdf) as a function of temperature. +Next we are going to analyze the trajectories in order to calculate the [[http://en.wikipedia.org/wiki/Radial_distribution_function|radial distribution function]] (rdf, $g(r)$) as a function of temperature.
-The rdf is typically denoted as $g(r)$.+
  
-You can use VMD to calculate the $g(r)$: In the VMD Main window open "Extensions -> Analysis" click on "Radial Pair Distribution function $g(r)$". In the appearing window use "Utilities -> Set unit cell dimensions" to let VMD know the lattice constant used (It is given in the input file for CP2K). After that in Selection 1 and 2 define the atomic types that you want to calculate the rdf for, for example with "element O".+VMD comes with an extension for exactly this purpose: In the VMD Main window open "Extensions -> Analysis" click on "Radial Pair Distribution function $g(r)$". In the appearing window use "Utilities -> Set unit cell dimensions" to let VMD know the simulation box you used. After that use Selection 1 and 2 to define the atomic types that you want to calculate the rdf for, for example "element H".
  
 <note>**TASK 3** <note>**TASK 3**
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   * Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph.   * Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph.
   * What are the differences in the height of the first peak?   * What are the differences in the height of the first peak?
-  * What does this say about the structure of the liquid and is this expected?+  * What does this say about the structure of the liquid and is this expected? (2P)
   * Compare to experimental data ''goo.ALS'' taken at 300 K.    * Compare to experimental data ''goo.ALS'' taken at 300 K. 
 </note> </note>
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   * What are the approximate frequencies of the stretching and bending modes?   * What are the approximate frequencies of the stretching and bending modes?
-  *  How do they compare to the normal mode frequencies of the isolated molecule? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum.+  *  How do they compare to the normal mode frequencies of the isolated molecule calculated previously? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum.
   * Perform a simulation with a larger time step (e.g. 1.5 fs). What is the effect on the spectrum? Provide graphs of both spectra in the report.   * Perform a simulation with a larger time step (e.g. 1.5 fs). What is the effect on the spectrum? Provide graphs of both spectra in the report.
   * Compare with Figure 3 in the paper of Praprotnik et al.   * Compare with Figure 3 in the paper of Praprotnik et al.
 </note> </note>
exercises/2014_uzh_molsim/h2o_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1