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exercises:2014_ethz_mmm:nacl_md [2014/05/30 10:59]
oschuett [1. Task: Observer NaCl dissociation]
exercises:2014_ethz_mmm:nacl_md [2014/10/15 12:42] (current)
oschuett exercise:nacl_md renamed to exercise:2014_ethz_mmm:nacl_md
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-===== 1. Task: Observer NaCl dissociation =====+=====Observer NaCl dissociation =====
 Perform a MD simulation of NaCl in water by running the input-file ''​NaCl_in_water.inp''​. ​ Perform a MD simulation of NaCl in water by running the input-file ''​NaCl_in_water.inp''​. ​
  
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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
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 <note tip> <note tip>
- You should run these calculations ​on 4 cores with bsub -n 4. + You should run this calculation ​on 4 cores with ''​bsub -n 4''​
 </​note>​ </​note>​
 ====== Required Files ====== ====== Required Files ======
exercises/2014_ethz_mmm/nacl_md.1401447566.txt.gz · Last modified: 2014/05/30 10:59 by oschuett