Differences

This shows you the differences between two versions of the page.

--- exercise:md_slab [2014/03/13 16:15] – dpasserone
+++ exercise:md_slab [2014/03/13 16:17] – dpasserone
@@ Line 23: / Line 23: @@
   - 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 35: @@
 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>