exercises:2017_uzh_acpc2:mol_sol
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exercises:2017_uzh_acpc2:mol_sol [2017/05/04 14:34] – [Water] jglan | exercises:2017_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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- | ====== | + | ====== |
===== Ramachandran plot ===== | ===== Ramachandran plot ===== | ||
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In particular, it has more than one long-lived conformation, | In particular, it has more than one long-lived conformation, | ||
- | The conformations of alanine | + | The conformations of glyala |
Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. | Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. | ||
the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. | the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. | ||
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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 '' |
</ | </ | ||
===== Water ===== | ===== Water ===== | ||
- | We have prepared a CP2K input file '' | + | We have prepared a CP2K input file '' |
- | < | + | Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders. |
+ | < | ||
* Check that the MD is energy conserving and // | * Check that the MD is energy conserving and // | ||
- | </ | + | |
- | + | ||
- | + | ||
- | Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders. | + | |
- | + | ||
- | < | + | |
- | + | ||
- | | + | |
- | * Why are they different from the initial ones? | + | |
* The initial atomic configuration stems from an equilibration run. At which temperature was the system (approximately) equilibrated? | * The initial atomic configuration stems from an equilibration run. At which temperature was the system (approximately) equilibrated? | ||
</ | </ | ||
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VMD comes with an extension for exactly this purpose: In the VMD Main window open " | VMD comes with an extension for exactly this purpose: In the VMD Main window open " | ||
- | < | + | < |
* Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph. | * Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph. | ||
* What are the differences in the height of the first peak? | * What are the differences in the height of the first peak? | ||
- | * What does this say about the structure of the liquid and is this expected? | + | * What does this say about the structure of the liquid and is this expected? |
* Compare to experimental data '' | * Compare to experimental data '' | ||
</ | </ | ||
- | Then we will calculate diffusion coefficient. | + | Then we will calculate diffusion coefficient. |
- | The diffusion | + | **$6D=\lim_{t\to\infty} |
- | $6D=\lim_{t\to\infty} | + | To evaluate this expression, all that is needed is to evaluate at each point in time in the calculation the average of the square of the distance that each atom has traveled since the start of the production phase of the dynamics, and examining the slope of this function at a long time. By storing the initial coordinates, |
+ | |||
+ | 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 RMSD for the water at 200K, 300K, 400K. | ||
+ | * Calculate their corresponding diffusion coefficients, | ||
+ | </note> | ||
===== 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. | ||
- Re-run the calculation using NVT ensemble with different TIMECON (500, 2000 fs) in the & | - Re-run the calculation using NVT ensemble with different TIMECON (500, 2000 fs) in the & |
exercises/2017_uzh_acpc2/mol_sol.1493908460.txt.gz · Last modified: 2020/08/21 10:15 (external edit)