exercises:2016_ethz_mmm:md_ala
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exercises:2016_ethz_mmm:md_ala [2016/03/16 23:25] – yakutovich | exercises:2016_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Molecular Dynamics simulation of a small molecule====== | ====== Molecular Dynamics simulation of a small molecule====== | ||
- | <note warning> | ||
- | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
- | |||
- | you@eulerX ~$ module load courses mmm vmd | ||
- | |||
- | you@eulerX ~$ mmm-init | ||
- | </ | ||
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* Have a look at the corresponding *.ener files (we suggest you to use gnuplot). | * Have a look at the corresponding *.ener files (we suggest you to use gnuplot). | ||
<note tip> | <note tip> | ||
- | Assignments | + | Assignments: |
- Do you see the energy conservation? | - Do you see the energy conservation? | ||
- Analyse the behavior of potential and kinetic energy, and the temperature. | - Analyse the behavior of potential and kinetic energy, and the temperature. | ||
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<note tip> | <note tip> | ||
- | Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them? | + | Assignments: |
+ | - Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them? | ||
+ | - Explore how the behaviour of the system changes with increasing of the temperature. Use inp.300 and change it in order to perform the simulations at 500K, 700K, 1000K. Comment on your observations. | ||
</ | </ | ||
exercises/2016_ethz_mmm/md_ala.1458170751.txt.gz · Last modified: 2020/08/21 10:15 (external edit)