exercises:2021_uzh_acpc2:ex02
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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 | ||
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===== 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 | ||
+ | </ | ||
< | < | ||
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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 | + | 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" | ||
< | < | ||
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{{ : | {{ : | ||
- | < | + | < |
Visualize the structure '' | Visualize the structure '' | ||
</ | </ | ||
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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. | ||
- | < | + | < |
- | - 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 '' | ||
</ | </ | ||
===== Glyala in water ===== | ===== 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 | + | Now, we will move to a more realistic system - Glyala |
- | <note important> | + | |
+ | 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, | ||
- | < | + | <note important> |
- | - Perform the molecular dynamics | + | |
+ | |||
+ | < | ||
+ | - 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, | ||
- Compute the O-O radial distribution function for water with acceptable statistics using 20 ps (after equilibration) of simulated time. | - 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 |
</ | </ | ||
<note tip> | <note tip> | ||
- | In last exercise, | + | From the last exercise, |
- | Using VMD, the O-O RDF for the water can 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.txt · Last modified: 2021/05/19 14:30 by jglan