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exercise:free_energy [2014/05/28 11:01] – oschuettexercises:2014_ethz_mmm:nacl_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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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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   - Click ''Save'' to store the distance-trajectory   - Click ''Save'' to store the distance-trajectory
  
-Plot the obtained distance-trajectory. Does the dissociation occur?+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
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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.1401274899.txt.gz · Last modified: 2020/08/21 10:14 (external edit)