exercises:2016_ethz_mmm:md_ala
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| exercises:2016_ethz_mmm:md_ala [2016/02/03 09:54] – external edit 127.0.0.1 | 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 | ||
| - | </ | ||
| Line 28: | Line 21: | ||
| Download the 4.1 exercise into your $HOME folder and unzip it: | Download the 4.1 exercise into your $HOME folder and unzip it: | ||
| <code bash> | <code bash> | ||
| - | you@eulerX ~$ wget http:// | + | you@eulerX ~$ wget http:// |
| - | you@eulerX ~$ unzip exercises:2015_ethz_mmm: | + | you@eulerX ~$ unzip exercises:2016_ethz_mmm: |
| you@eulerX ~$ cd exercise_4.1 | you@eulerX ~$ cd exercise_4.1 | ||
| </ | </ | ||
| Line 75: | Line 68: | ||
| * 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 | ||
| Line 161: | Line 154: | ||
| <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.1454493256.txt.gz · Last modified: 2020/08/21 10:15 (external edit)