exercises:2018_uzh_acpc2:mol_sol
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exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:07] – [Water] jglan | exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:14] – [Water] jglan | ||
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[[http:// | [[http:// | ||
- | We have prepared a CP2K input file '' | + | We have prepared a CP2K input file '' |
+ | <note important> | ||
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* Does IR or dielectric constant match the experimenal value? If not, why? | * Does IR or dielectric constant match the experimenal value? If not, why? | ||
</ | </ | ||
- | |||
===== Ramachandran plot ===== | ===== Ramachandran plot ===== | ||
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Visualize the structure '' | Visualize the structure '' | ||
</ | </ | ||
+ | |||
+ | <note important>// | ||
+ | |||
With this knowledge at hand, | With this knowledge at hand, | ||
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< | < | ||
- | - The atomic indices defining the dihedral indices in the input file '' | + | - The atomic indices defining the dihedral indices in the input file '' |
- Use '' | - Use '' | ||
- 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. | 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. |
exercises/2018_uzh_acpc2/mol_sol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1