exercises:2018_ethz_mmm:h2o_md
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exercises:2018_ethz_mmm:h2o_md [2018/03/02 11:13] – dpasserone | exercises:2018_ethz_mmm:h2o_md [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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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< | < | ||
./ | ./ | ||
- | ./mean_square_displ.py T300.xyz 3 10 100 | + | ./mean_square_disp.py T300.xyz 3 10 100 |
./ | ./ | ||
</ | </ | ||
+ | Remember: to display the **png** files, the command is < | ||
<note important> | <note important> | ||
- | - look at the file T300-1.ener at the end of the simulation. It contains several quantities. Check the header | + | - 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 < | - 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? | - Compare the values of the diffusion coefficient with the two methods. Are they compatible? | ||
- Look at the trajectories with vmd. Why are the particles " | - Look at the trajectories with vmd. Why are the particles " | ||
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- Copy md300.in into md400.in and change to 400 in the two places. 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. | - Check the temperature dependence of the diffusion coefficient. Plot the result. | ||
- | </ | ||
</ | </ | ||
exercises/2018_ethz_mmm/h2o_md.1519989197.txt.gz · Last modified: 2020/08/21 10:15 (external edit)