exercises:2014_uzh_molsim:h2o_md
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exercise:mm_uzh:h2o_md [2014/05/02 17:16] – talirz | exercise:mm_uzh:h2o_md [2014/05/06 12:50] – talirz | ||
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* Check that the MD is energy conserving and // | * Check that the MD is energy conserving and // | ||
- | * FIXME additional question | ||
</ | </ | ||
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</ | </ | ||
- | Now we are going to analyze the trajectories in order to calculate the [[http:// | + | Next we are going to analyze the trajectories in order to calculate the [[http:// |
- | The rdf is typically denoted as $g(r)$. | + | |
- | You can use VMD to calculate the $g(r)$: In the VMD Main window open " | + | VMD comes with an extension for exactly this purpose: In the VMD Main window open " |
< | < | ||
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* 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 '' | ||
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In MD simulations, | In MD simulations, | ||
- | Repeat the MD at 300 K, but now uncomment the ''& | + | Repeat the MD at 300 K, but now uncomment the ''& |
- | Once the simulation is finished, calculate the autocorrelation function. | + | |
- | We have provided a short Fortran program '' | + | We have provided a short Fortran program '' |
+ | Use the '' | ||
<code bash> | <code bash> | ||
gfortran dipole_correlation.f90 -o dipole_correlation.x | gfortran dipole_correlation.f90 -o dipole_correlation.x | ||
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< | < | ||
- | * What are the estimate | + | * What are the approximate |
* How do they compare to the normal mode frequencies of the isolated molecule? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum. | * How do they compare to the normal mode frequencies of the isolated molecule? 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. | * 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. | * Compare with Figure 3 in the paper of Praprotnik et al. | ||
</ | </ |
exercises/2014_uzh_molsim/h2o_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1