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exercises:2014_ethz_mmm:nacl_md [2014/05/28 10:44]
oschuett created
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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 +====== Observer NaCl dissociation ======
 +
 +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.
 +This can be done in the following way:
 +  - Load the trajectory with VMD
 +  - Select ''​Extensions''​ -> ''​Analysis''​ -> ''​Radial Pair Distribution Function''​ from the menu
 +  - 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
 +  - Click successively on the Na and the Cl atom
 +  - 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 ======
 <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
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 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.1401273848.txt.gz ยท Last modified: 2014/05/28 10:44 by oschuett