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--- exercises:2021_uzh_acpc2:ex02 [2021/05/11 09:41] – jglan
+++ exercises:2021_uzh_acpc2:ex02 [2021/05/19 14:30] (current) – jglan
@@ Line 5: / Line 5: @@
 We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parameterized by [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|Praprotnik et al.]]).
-<note important>Download {{ :exercises:2019_uzh_acpc2:water.zip |water.zip}} and extract it.</note>
+<note important>Download {{ :exercises:2021_uzh_acpc2:water.zip |}} and extract it.</note>
-<code> wget https://www.cp2k.org/_media/exercises:2019_uzh_acpc2:water.zip
+<code>wget https://www.cp2k.org/_media/exercises:2021_uzh_acpc2:water.zip
 unzip water.zip
 </code>
@@ Line 32: / Line 32: @@
 Finally, if you take care of the above, the value of D is obtained from the slope, at a long time, of the right-hand side of the above equation (also be careful with the units).
-Once again, VMD comes with an extension for exactly this purpose: In the VMD Main window open “Extensions → Analysis” click on “RMSD Trajectory Tool”. In the appearing window use “all” to let VMD know the molecule you want to track. Tick "Plot", and press "RMSD". This will plot the RMSD for the water system.
+Once again, VMD comes with an extension for exactly this purpose: In the VMD
+Main window open “Extensions → Analysis” click on “RMSD Trajectory Tool”. In the
+appearing window change “protein” to “all” to let VMD know the molecule you want
+to track. Press "RMSD" to run the analysis (Note: this might take a while!).
+Finally, use "File -> Plot data" to plot the RMSD for the water system.
 <note>**TASK 3**