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--- exercise:md_slab [2014/03/13 16:15] – dpasserone
+++ exercise:md_slab [2014/04/21 15:36] – ibethune
@@ Line 7: / Line 7: @@
 **/cluster/home03/matl/danielep/LECTURE4/EXERCISE_4.2/**
+or download from the wiki: {{exercise:exercise_4.2.tar.gz|exercise_4.2.tar.gz}}
 First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat.
@@ Line 23: / Line 25: @@
   - 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 37: @@
 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>