exercises:2021_uzh_acpc2:ex02
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
exercises:2021_uzh_acpc2:ex02 [2021/05/04 07:06] – [Glyala in water] mrossmannek | exercises:2021_uzh_acpc2:ex02 [2021/05/19 14:30] (current) – jglan | ||
---|---|---|---|
Line 2: | Line 2: | ||
===== Water ===== | ===== 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/ |
We have prepared a CP2K input file '' | We have prepared a CP2K input file '' | ||
- | <note important> | + | <note important> |
+ | < | ||
+ | unzip water.zip | ||
+ | </ | ||
< | < | ||
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). | 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 | + | 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 | ||
+ | to track. | ||
+ | Finally, use "File -> Plot data" | ||
< | < | ||
Line 82: | Line 90: | ||
{{ : | {{ : | ||
- | < | + | < |
Visualize the structure '' | Visualize the structure '' | ||
</ | </ | ||
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. | With this knowledge at hand, we will fix the dihedral angles and perform geometry optimization for all remaining degrees of freedom. | ||
- | < | + | < |
- | - The atomic indices defining the dihedral indices in the input file '' | + | - The atomic indices defining the dihedral indices in the input file '' |
- Use the provided bash script, '' | - Use the provided bash script, '' | ||
- Use gnuplot to plot the potential energy surface (we have provided a script '' | - Use gnuplot to plot the potential energy surface (we have provided a script '' | ||
Line 106: | Line 114: | ||
- | < | + | < |
- Perform the MD simulation using an NVT ensemble at 300K. Change TIMECON (i.e.500, 2000 fs) in the & | - Perform the MD simulation using an NVT ensemble at 300K. Change TIMECON (i.e.500, 2000 fs) in the & | ||
- Determine from which step the system is equilibrated, | - Determine from which step the system is equilibrated, | ||
Line 115: | Line 123: | ||
<note tip> | <note tip> | ||
- | 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 < | However, using VMD, the O-O RDF for the water can still be easily calculated. In the < | ||
</ | </ | ||
+ |
exercises/2021_uzh_acpc2/ex02.1620111984.txt.gz · Last modified: 2021/05/04 07:06 by mrossmannek