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--- exercise:mm_uzh:h2o_md [2014/05/02 17:20] – talirz
+++ exercise:mm_uzh:h2o_md [2014/05/06 12:50] – talirz
@@ Line 8: / Line 8: @@
   * Check that the MD is energy conserving and //well-behaved//.
-  * FIXME additional question
 </note>
@@ Line 21: / Line 20: @@
 </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**
@@ Line 30: / Line 28: @@
   * 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 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.
 </note>