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 [2018/03/02 11:14] – dpasserone | ||
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| <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 " | ||
| Line 258: | Line 259: | ||
| - 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1