exercises:2014_ethz_mmm:nacl_md
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exercises:2014_ethz_mmm:nacl_md [2014/05/29 11:55] vondele |
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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| 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 ? | 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> | ||
exercises/2014_ethz_mmm/nacl_md.1401364512.txt.gz · Last modified: 2014/05/29 11:55 by vondele
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