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--- exercise:md_slab [2014/03/13 16:10] – created 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 29: / Line 27: @@
 Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp).
+<note important>Discuss the differences in the density profile. What do you expect to see in vmd?
+</note>
+Now, use vmd to look at the trajectories. As you launch vmd,
+you can (assignment):
+<note important>
+- source a pbc.vmd file which includes the definition of the periodic box
+- draw the box: **draw pbcbox** in the Tk console
+- wrap all atoms in the periodic box: **pbc wrap -first first -last last**
+- "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>