Differences

This shows you the differences between two versions of the page.

--- exercise:mm_uzh:h2o_md [2014/05/02 17:20] – talirz
+++ exercise:mm_uzh:h2o_md [2014/05/05 18:01] – talirz
@@ Line 21: / Line 21: @@
 </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**