exercises:2018_ethz_mmm:h2o_md
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exercises:2018_ethz_mmm:h2o_md [2018/03/02 11:01] – dpasserone | exercises:2018_ethz_mmm:h2o_md [2018/03/02 15:36] – dpasserone | ||
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Download the 2.1 exercise into your **EXERCISES** folder and unzip it. | Download the 2.1 exercise into your **EXERCISES** folder and unzip it. | ||
- | < | + | |
- | max@qmobile: | + | |
- | max@qmobile: | + | |
- | max@qmobile: | + | |
- | max@qmobile: | + | |
- | </ | + | |
This exercise is mostly taken by a [[https:// | This exercise is mostly taken by a [[https:// | ||
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- Run the **md300.in**: | - Run the **md300.in**: | ||
- Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function | - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function | ||
- | - Extract the diffusion coefficients and compare the two approaches: | + | - Extract the diffusion coefficients and compare the two approaches |
- | < | + | < |
- | vel_autocorr_plot.py vel_autocorr.out | + | ./vel_autocorr_plot.py vel_autocorr.out |
- | mean_square_displ.py T300.xyz 3 10 100 | + | ./ |
- | msd_fit_and_plot.py mean_square_disp.out | + | ./msd_fit_and_plot.py mean_square_disp.out |
</ | </ | ||
- | + | Remember: to display the **png** files, the command is < | |
+ | <note important> | ||
+ | - look at the file T300-1.ener at the end of the simulation. It contains several quantities. Check the header! | ||
+ | - Using gnuplot, check the stability of the MD, you can also use < | ||
+ | - How do you interpret the oscillation of the potential energy? And of temperature? | ||
+ | - Compare the values of the diffusion coefficient with the two methods. Are they compatible? | ||
+ | - Look at the trajectories with vmd. Why are the particles " | ||
+ | - Copy md300.in into md200.in and change the system name and the initial temperature. Run the md. What is the final temperature? | ||
+ | - Copy md300.in into md400.in and change to 400 in the two places. Run the md. What is the final temperature? | ||
+ | - Check the temperature dependence of the diffusion coefficient. Plot the result. | ||
</ | </ | ||
exercises/2018_ethz_mmm/h2o_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1