exercises:2018_uzh_acpc2:mol_sol
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exercises:2018_uzh_acpc2:mol_sol [2018/05/03 12:39] – jglan | exercises:2018_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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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* Plot RMSD for the water at 300K and calculate corresponding diffusion coefficient, | * Plot RMSD for the water at 300K and calculate corresponding diffusion coefficient, | ||
</ | </ | ||
+ | <note important> | ||
- | In this exercise, we will compute the vibrational spectrum, and dielectric constant of water based on molecular dynamics. The spectra for water are available in this paper [[https:// | + | We will compute the vibrational spectrum, and dielectric constant of water based on molecular dynamics. The spectra for water are available in this paper [[https:// |
\begin{equation} | \begin{equation} | ||
- | A(\omega)\propto{\int<{\mu}({\tau}){\mu}(t+{\tau})}_{\tau}>e^{-i{\omega}t}d{t}}, | + | A(\omega)\propto{\int\langle{\mu}({\tau}){\mu}(t+{\tau})\rangle_{\tau}e^{-i{\omega}t}d{t}}, |
+ | \label{eq: | ||
\end{equation} | \end{equation} | ||
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\end{equation} | \end{equation} | ||
+ | Compile the FORTRAN code, and execute the program | ||
+ | < | ||
+ | gfortran cpt_ir_diele.f90 -o cpt_ir_diele.o | ||
+ | ./ | ||
+ | </ | ||
+ | < | ||
+ | * Compute the IR spectrum and plot it, match the frequencies with vibrational mode. | ||
+ | * Compute the dielectric constant of water at 300K. | ||
+ | * 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. | ||
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< | < | ||
- | - Perform the molecular dynamics simulation using NVT ensemble at 300K. | + | - Perform the molecular dynamics simulation using NVT ensemble at 300K. Change |
- | - Re-run the calculation using NVT ensemble with different | + | |
- 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) | ||
</ | </ | ||
exercises/2018_uzh_acpc2/mol_sol.1525351197.txt.gz · Last modified: 2020/08/21 10:15 (external edit)