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--- exercise:md_slab [2014/03/13 16:15] – dpasserone
+++ exercises:2014_ethz_mmm:md_slab [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 4: / Line 4: @@
 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.
@@ Line 23: / Line 21: @@
   - 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.
-  **- 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...).
 </note>
@@ Line 35: / Line 33: @@
 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>