exercises:2015_uzh_molsim:h2o_md
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+ | ====== Molecular dynamics of liquid $\text{H}_2\text{O}$ ====== | ||
+ | ===== Radial distribution function ===== | ||
+ | |||
+ | We have prepared a CP2K input file '' | ||
+ | |||
+ | < | ||
+ | |||
+ | * 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. | ||
+ | |||
+ | < | ||
+ | |||
+ | * What are the final average temperatures in each of the simulations? | ||
+ | * 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? | ||
+ | </ | ||
+ | |||
+ | Next we are going to analyze the trajectories in order to calculate the [[http:// | ||
+ | |||
+ | 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. | ||
+ | * 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? (2P) | ||
+ | * Compare to experimental data '' | ||
+ | </ | ||
+ | |||
+ | ===== Infrared spectrum ===== | ||
+ | |||
+ | Due to the partial charges on the oxygen and hydrogen atoms, both the stretching and the bending motion of the $\text{H}_2\text{O}$ molecule give rise to oscillations in its dipole moment. | ||
+ | In MD simulations, | ||
+ | |||
+ | Repeat the MD at 300 K, but now uncomment the ''& | ||
+ | |||
+ | We have provided a short Fortran program '' | ||
+ | Use the '' | ||
+ | <code bash> | ||
+ | gfortran dipole_correlation.f90 -o dipole_correlation.x | ||
+ | ./ | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | |||
+ | * What are the approximate frequencies of the stretching and bending modes? | ||
+ | * How do they compare to the normal mode frequencies of the isolated molecule calculated previously? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum. | ||
+ | * Perform a simulation with a larger time step (e.g. 1.5 fs). What is the effect on the spectrum? Provide graphs of both spectra in the report. | ||
+ | * Compare with Figure 3 in the paper of Praprotnik et al. | ||
+ | </ |