User Tools

Site Tools


exercises:2014_ethz_mmm:nacl_md

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
Last revisionBoth sides next revision
exercise:free_energy [2014/05/28 10:44] – created oschuettexercise:2014_ethz_mmm:nacl_md [2014/10/15 12:42] – exercise:nacl_md renamed to exercise:2014_ethz_mmm:nacl_md oschuett
Line 1: Line 1:
 +====== 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
Line 353: 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1