exercises:2017_uzh_acpc2:mol_sol
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
exercises:2017_uzh_acpc2:mol_sol [2017/05/04 14:56] – [Water] jglan | exercises:2017_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== | + | ====== |
===== Ramachandran plot ===== | ===== Ramachandran plot ===== | ||
Line 6: | Line 6: | ||
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. | ||
Line 26: | Line 26: | ||
- 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. | 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 // | ||
* What are the final average temperatures in each of the simulations? | * What are the final average temperatures in each of the simulations? | ||
Line 43: | Line 43: | ||
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. | ||
Line 58: | Line 58: | ||
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 " | 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. | * Plot RMSD for the water at 200K, 300K, 400K. | ||
* Calculate their corresponding diffusion coefficients, | * Calculate their corresponding diffusion coefficients, | ||
Line 69: | Line 69: | ||
- | < | + | < |
- 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.1493909791.txt.gz · Last modified: 2020/08/21 10:15 (external edit)