exercises:2016_ethz_mmm:md_ala
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exercises:2016_ethz_mmm:md_ala [2016/03/16 22:59] – yakutovich | exercises:2016_ethz_mmm:md_ala [2016/03/17 15:31] – yakutovich | ||
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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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Now you will perform a constant Temperature simulations, | Now you will perform a constant Temperature simulations, | ||
- | < | + | < |
Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi> | Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi> | ||
</ | </ | ||
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you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100 | you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100 | ||
</ | </ | ||
- | * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, but **put 300 K** instead of 100 K | + | * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, except of the temperature which you set as ** 300 K** instead of 100 K |
<code bash> | <code bash> | ||
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300 | you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300 | ||
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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? | ||
</ | </ | ||
exercises/2016_ethz_mmm/md_ala.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1