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exercises:2014_ethz_mmm:nacl_md [2014/05/28 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
Line 1: Line 1:
-===== 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''​. ​
  
 Use VMD to calculate the Na-Cl distance for each frame of the trajectory. Use VMD to calculate the Na-Cl distance for each frame of the trajectory.
 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 
-  - Select ''​Mouse''​ -> ''​Label''​ -> ''​Bonds''​ from the menu +  - Set the lengths a,b, and c to the value 12.413800, and click ''​Set unit cell''​ 
-  - Click successively on the Na and the Cl atom. +  - Close the $g(r)$-dialog 
-  - Select ''​Graphics''​ -> ''​Labels...''​ from the menu. +  - Fold back periodic images by typing: ''​pbc wrap -centersel "​element Na" -center com -all''​ 
-  - Select ''​Bonds''​ from the drop-down on the top left. +  - Select ''​Mouse''​ -> ''​Label''​ -> ''​Bonds''​ from the menu 
-  - Go to the tab ''​Graph''​. +  - Click successively on the Na and the Cl atom 
-  - Click ''​Save''​ to store the distance-trajectory.+  - Select ''​Graphics''​ -> ''​Labels...''​ from the menu 
 +  - Select ''​Bonds''​ from the drop-down on the top left 
 +  - Go to the tab ''​Graph''​ 
 +  - Click ''​Save''​ to store the distance-trajectory 
 + 
 +Plot the obtained ​distance-trajectory. ​Does the dissociation occur? If it occurs, does the actual transition happens quickly ? Is dissociation a likely or rare event ? Do you expect an activation energy ?
  
 +<note tip>
 + You should run this calculation on 4 cores with ''​bsub -n 4''​. ​
 +</​note>​
 ====== Required Files ====== ====== Required Files ======
 <code - NaCl_in_water.inp>​ <code - NaCl_in_water.inp>​
 &GLOBAL &GLOBAL
-  PROJECT ​run-NACL-FREE-MYSEED+  PROJECT ​NaCl-Free
   RUN_TYPE MD   RUN_TYPE MD
 &END GLOBAL &END GLOBAL
Line 369: Line 378:
 Cl    1.3489457703231567E+01 ​   1.0346547591020910E+01 ​   1.2149103773398551E+01 CLM Cl    1.3489457703231567E+01 ​   1.0346547591020910E+01 ​   1.2149103773398551E+01 CLM
      &​END COORD      &​END COORD
 +     &​COLVAR
 +       &​DISTANCE
 +         ATOMS 190 191
 +       &​END DISTANCE
 +       &​PRINT
 +       &​END
 +    &END COLVAR
     &​TOPOLOGY     &​TOPOLOGY
       CONNECTIVITY GENERATE       CONNECTIVITY GENERATE
exercises/2014_ethz_mmm/nacl_md.1401274780.txt.gz · Last modified: 2014/05/28 10:59 by oschuett