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exercise:md_slab [2014/03/13 16:15] dpasseroneexercise:2014_ethz_mmm:md_slab [2014/10/15 13:29] oschuett
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 This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g(r) at various temperatures. This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g(r) at various temperatures.
  
-As usual, create a new directory and copy the files from: +As usual, create a new directory and download the files from the wiki{{exercise_4.2.tar.gz|exercise_4.2.tar.gz}}
- +
-**/cluster/home03/matl/danielep/LECTURE4/EXERCISE_4.2/**+
  
 First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat.
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   - Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory.    - Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory. 
   - Run it and see the differences to the first profile.   - Run it and see the differences to the first profile.
-  **- Do the same excluding the first 10 frames.** +  - Do the same excluding the first 10 frames.
   - Explain those differences, based on what you see in the *.ener file (energies, temperature...).   - Explain those differences, based on what you see in the *.ener file (energies, temperature...).
 </note> </note>
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 you can (assignment): you can (assignment):
  
-  <note important>- source a pbc.vmd file which includes the definition of the periodic box +<note important> 
-  - draw the box: **draw pbcbox** in the Tk console +- source a pbc.vmd file which includes the definition of the periodic box 
-  - wrap all atoms in the periodic box: **pbc wrap -first first -last last** +- draw the box: **draw pbcbox** in the Tk console 
-  - "play" with representations: try to color the surface atoms in one color, the bulk ones in another color. +- wrap all atoms in the periodic box: **pbc wrap -first first -last last** 
-  - Using the "radial distribution function" plugin from the extension menu, draw the g(r) of the system. Discuss it for 700, 1100, and 1300 K. +- "play" with representations: try to color the surface atoms in one color, the bulk ones in another color. 
 +- Using the "radial distribution function" plugin from the extension menu, draw the g(r) of the system. Discuss it for 700, 1100, and 1300 K. 
 </note> </note>
- 
exercises/2014_ethz_mmm/md_slab.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1