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--- exercises:2015_ethz_mmm:md_slab [2015/03/09 17:03] – yakutovich
+++ exercises:2015_ethz_mmm:md_slab [2015/03/11 14:00] – yakutovich
@@ Line 36: / Line 36: @@
 </note>
-Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp):
+  * Perform **consequently** a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp):
 <code bash>
 you@eulerX exercise_4.2$ bsub cp2k.popt -i 1100.inp -o 1100.out
 you@eulerX exercise_4.2$ bsub cp2k.popt -i 1300.inp -o 1300.out
 </code>
+  * And again analyze these trajectories using the script histo_z:
+<code bash>
+you@eulerX exercise_4.2$ ./histo_z 1100-1-pos.xyz
+you@eulerX exercise_4.2$ ./histo_z 1300-1-pos.xyz
+</code>
 <note tip>
@@ Line 46: / Line 53: @@
 </note>
-Now, use vmd to look at the trajectories. As you launch vmd,
+  * Now, use vmd to look at the trajectories. As you launch vmd,
 in Tk console you can:
 Load a pbc.vmd file which includes the definition of the periodic box
-<code>
+<code tcl>
-source pbc.vmd
+vmd> source pbc.vmd
 </code>
 Draw the box:
-<code>
+<code tcl>
-draw pbcbox
+vmd> draw pbcbox
 </code>
 Wrap all atoms in the periodic box:
-<code>
+<code tcl>
-pbc wrap -first first -last last
+vmd> pbc wrap -first first -last last
 </code>
-Try to play with representations: color the surface atoms in one color, the bulk ones in another color.
+  * Try to play with representations: 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.
+  * Using the "radial distribution function" plugin from the extension menu, draw the g(r) of the system.
 <note tip>
  Discuss radial distribution function for 700, 1100, and 1300 K.
 </note>