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exercise:nacl_md [2014/05/30 12:19] – [Observer NaCl dissociation] oschuettexercises:2014_ethz_mmm:nacl_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 This can be done in the following way: This can be done in the following way:
   - Load the trajectory with VMD   - Load the trajectory with VMD
-  - Setup the box by typing: ''vmd pbc set {12.4138  12.4138  12.4138}'' +  - Select ''Extensions'' -> ''Analysis'' -> ''Radial Pair Distribution Function'' from the menu 
-  - Fold back periodic images by typing: ''vmd > pbc wrap''+  - Within the $g(r)$-dialog select ''Utilities'' -''Set unit cell dimensions'' from the menu 
 +  - Set the lengths a,b, and c to the value 12.413800, and click ''Set unit cell'' 
 +  - Close the $g(r)$-dialog 
 +  - Fold back periodic images by typing: ''pbc wrap -centersel "element Na" -center com -all''
   - Select ''Mouse'' -> ''Label'' -> ''Bonds'' from the menu   - Select ''Mouse'' -> ''Label'' -> ''Bonds'' from the menu
   - Click successively on the Na and the Cl atom   - Click successively on the Na and the Cl atom
exercises/2014_ethz_mmm/nacl_md.1401452387.txt.gz · Last modified: 2020/08/21 10:14 (external edit)