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--- exercises:2021_uzh_acpc2:installation [2021/04/13 13:21] – Update instructions mrossmannek
+++ exercises:2021_uzh_acpc2:installation [2021/04/14 12:30] (current) – [Part II: Loading and running a program] Update VMD instructions mrossmannek
@@ Line 162: / Line 162: @@
-=== Using VMD ===
+=== Getting the input data ===
-Now, we are ready to visualize the previously computed trajectory with VMD.
+Before you can try out VMD, we must get some data to visualize.
+For now, we simply want to view all the Argon atoms from our previous simulation.
+To do so, we need to extract their coordinates from the input file.
+The easiest solution to this, is to copy them into an [[https://en.wikipedia.org/wiki/XYZ_file_format|XYZ coordinate file]]:
+<code>
+cp argon.inp argon.xyz
+</code>
+Now, you must remove everything but the atoms coordinates.
+You should end up with 108 lines in your file, each containing the coordinate of a single Ar atom.
-<note todo>Update the following</note>
+To make this a fully functional ''XYZ'' file, you must change the top of the file to be the following:
+  - The number of atoms on the first line
+  - A blank line (or a comment)
+  - The rest of the file
+<code>
+
+Ar -8.53869012951987116 -15.5816257770688615 2.85663672298278293
+...
+</code>
+=== Using VMD ===
+Now, we are ready for our first visualization with VMD.
 Open VMD. From ''File -> New molecule...'' open the file with the ''.xyz'' extension. Go to ''Graphics -> Representations..'' and change the Drawing Method to VDW. On the VMD shell type the following commands to define the unit cell of the system and wrap the atoms back to their original unit cell.
@@ Line 175: / Line 196: @@
 </code>
-A snapshot of the molecular dynamics trajectory should approximately look like this:
+<note tip>''pbc'' stands for //periodic boundary conditions// and you can also find the box edge lengths in the input file under ''FORCE_EVAL/SUBSYS/CELL/ABC''</note>
-{{:exercises:2018_uzh_acpc2:argon_liq_first_sim.png?400 |}}
+<note tip>
+If you prefer to load the file and set the drawing methods via commands, you can do the following:
+<code>
+mol new argon.xyz
+mol modstyle 0 0 vdw
+</code>
+The first commands loads the file ''argon.xyz''.
+The second command assumes this is the first file you load (the first index ''0'') and that this file contains only a single molecule (the second index ''0'').
+</note>
+A snapshot of the molecular dynamics trajectory should approximately look like this:
+{{:exercises:2018_uzh_acpc2:argon_liq_first_sim.png?400 |}}
 =====  Plotting tools =====