exercises:2018_uzh_acpc2:mol_sol
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exercises:2018_uzh_acpc2:mol_sol [2018/05/03 13:03] – jglan | exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:12] – [Ramachandran plot] 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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* 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> | ||
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:// | ||
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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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< | < | ||
- | - 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1