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--- exercises:2021_uzh_acpc2:ex02 [2021/05/04 07:01] – [Ramachandran plot] Minor updates mrossmannek
+++ exercises:2021_uzh_acpc2:ex02 [2021/05/19 14:30] (current) – jglan
@@ Line 2: / Line 2: @@
 ===== Water =====
-[[http://www1.lsbu.ac.uk/water/water_models.html|Water molecular models]] are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be used in the simulations.
+[[http://www.idc-online.com/technical_references/pdfs/chemical_engineering/Water_models.pdf|Water molecular models]] are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be used in the simulations.
 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**
@@ Line 28: / 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**
@@ Line 82: / Line 90: @@
 {{  :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.
 </note>
@@ Line 91: / Line 99: @@
 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 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?
 </note>
 ===== Glyala in water =====
-Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory.
-The initial geometry provided in the PDB file is a glyala molecule solvated by 73 water molecules. The geometry is not equilibrated. You need first to equilibrate the system at 300K. When the system is equilibrated, you need to analysis the result.
+Now, we will move to a more realistic system - Glyala in water. We will preform a MD simulation of glyala in water and save the trajectory.
-<note important>Download the {{ exercises:2017_uzh_acpc2:glyala_water.tar.gz |glyala_water.tar.gz}} and extract it. </note>
+The initial geometry provided in the PDB file is a glyala molecule solvated by 73 water molecules. The geometry is not equilibrated. Thus, you first need to equilibrate the system at 300K. When the system is equilibrated, you need to analyze the result.
-<note>**TASK 6**
+<note important>Download the {{ exercises:2017_uzh_acpc2:glyala_water.tar.gz |glyala_water.tar.gz}} and extract it. See above on how to extract a ''tar''-archive.</note>
-   - Perform the molecular dynamics simulation using NVT ensemble at 300K. Change TIMECON (i.e.500, 2000 fs) in the &THERMOSTAT section.
+<note>**TASK 7**
+   - 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.
    - Compute the O-O radial distribution function for water with acceptable statistics using 20 ps (after equilibration) of simulated time.
-   - Determine the solvation shell by calculating RDF of g$_{CO}$ (carbon atoms from glyala and oxygen atoms from water)
+   - Determine the solvation shell by calculating the RDF of g$_{CO}$ (carbon atoms from glyala and oxygen atoms from water)
 </note>
 <note tip>**Tip for O-O RDF for water**
-In last exercise, one already knew how to calculate the RDF for the Argon system. In TASK3, you need to calculate the RDF only for water instead of whole system. Since the glyala contain two oxygen atoms, it is not reasonable to include the oxygen atoms in glyala molecule if we are only interested in 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.
-Using VMD, the O-O RDF for the water can be easily calculated. In the <code> Selection 1, Selection 2 </code>, one need to specify <code> element O and not same residue as element C </code> 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>