exercises:2015_ethz_mmm:md_ala
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exercises:2015_ethz_mmm:md_ala [2015/03/13 08:39] – yakutovich | exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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<note warning> | <note warning> | ||
TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
- | you@eulerX ~$ module load courses mmm vmd ; mmm-init | + | |
+ | you@eulerX ~$ module load courses mmm vmd | ||
+ | |||
+ | you@eulerX ~$ mmm-init | ||
</ | </ | ||
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You will start from a configuration already computed in the second lecture (**inp.a.pdb**) which is included in the repository of this exercise as well. | You will start from a configuration already computed in the second lecture (**inp.a.pdb**) which is included in the repository of this exercise as well. | ||
Update the following part of the file **inp.nve** for the first simulation: | Update the following part of the file **inp.nve** for the first simulation: | ||
- | <note tip> | + | |
- | To get more information, | + | |
- | http:// | + | |
- | </ | + | |
<code - md_part.inp.nve> | <code - md_part.inp.nve> | ||
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</ | </ | ||
+ | <note tip> | ||
+ | To get more information, | ||
+ | http:// | ||
+ | </ | ||
* Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. Use 100 K as an initial temperature! | * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. Use 100 K as an initial temperature! | ||
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</ | </ | ||
- | Edit the inp.100 file (Put there: | + | Edit the inp.100 file (Put there: |
<code bash> | <code bash> | ||
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 |
exercises/2015_ethz_mmm/md_ala.1426235985.txt.gz · Last modified: 2020/08/21 10:14 (external edit)