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exercises:2021_uzh_acpc2:ex02 [2021/05/04 07:34] – [Water] Fix dead link mrossmannekexercises:2021_uzh_acpc2:ex02 [2021/05/19 14:30] (current) – jglan
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 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.]]). 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:2021_uzh_acpc2:water.zip 
 +unzip water.zip 
 +</code> 
  
 <note>**TASK 1** <note>**TASK 1**
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 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). 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** <note>**TASK 3**
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 {{  :exercises:2017_uzh_acpc2:vmdscene.png ?direct&400 |}} {{  :exercises:2017_uzh_acpc2:vmdscene.png ?direct&400 |}}
  
-<note>**TASK 1**+<note>**TASK 5**
 Visualize the structure ''glyala.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles. Visualize the structure ''glyala.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles.
 </note> </note>
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 With this knowledge at hand, we will fix the dihedral angles and perform geometry optimization for all remaining degrees of freedom. With this knowledge at hand, we will fix the dihedral angles and perform geometry optimization for all remaining degrees of freedom.
  
-<note>**TASK 2**+<note>**TASK 6**
  
-  - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by the atomic indices determined in //Task 1//. +  - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by the atomic indices determined in //Task 5//. 
   - Use the provided bash script, ''perform-gopt.sh'', to perform the grid of geometry optimizations.   - Use the provided bash script, ''perform-gopt.sh'', to perform the grid of geometry optimizations.
   - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp'') <code> gnuplot > load "epot.gp"</code>What are the two most favored conformations?   - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp'') <code> gnuplot > load "epot.gp"</code>What are the two most favored conformations?
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-<note>**TASK 3**+<note>**TASK 7**
    - Perform the MD simulation using an NVT ensemble at 300K. Change TIMECON (i.e.500, 2000 fs) in the &THERMOSTAT section.    - Perform the MD simulation using an NVT ensemble at 300K. Change TIMECON (i.e.500, 2000 fs) in the &THERMOSTAT section.
    - Determine from which step the system is equilibrated, plot the calculated properties and explain why.    - Determine from which step the system is equilibrated, plot the calculated properties and explain why.
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 <note tip>**Tip for O-O RDF for water** <note tip>**Tip for O-O RDF for water**
  
-From the last exercise, you already know how to calculate the RDF for the Argon system. However, in TASK 3 you need to calculate the RDF only for water instead of the whole system. Since the glyala molecule contains two oxygen atoms itself, it is not reasonable to include these oxygen atoms of glyala if we are only interested in the O-O RDF for water.+From the last exercise, you already know how to calculate the RDF for the Argon system. However, in TASK 7 you need to calculate the RDF only for water instead of the whole system. Since the glyala molecule contains two oxygen atoms itself, it is not reasonable to include these oxygen atoms of glyala if we are only interested in the O-O RDF for water.
 However, using VMD, the O-O RDF for the water can still be easily calculated. In the <code> Selection 1, Selection 2 </code>, you need to specify <code> element O and not same residue as element C </code> in order to exclude the oxygen atoms present in glyala. The frames should start from the beginning of production run. However, using VMD, the O-O RDF for the water can still be easily calculated. In the <code> Selection 1, Selection 2 </code>, you need to specify <code> element O and not same residue as element C </code> in order to exclude the oxygen atoms present in glyala. The frames should start from the beginning of production run.
 </note> </note>
 +
exercises/2021_uzh_acpc2/ex02.1620113691.txt.gz · Last modified: 2021/05/04 07:34 by mrossmannek