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--- exercise:md_slab [2014/03/13 16:10] – created dpasserone
+++ exercise:md_slab [2014/03/13 16:15] – dpasserone
@@ Line 29: / Line 29: @@
 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>