exercises:2015_ethz_mmm:md_ala
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exercises:2015_ethz_mmm:md_ala [2015/03/11 10:33] – yakutovich | exercises:2015_ethz_mmm:md_ala [2015/03/13 15:16] – yakutovich | ||
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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 | ||
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<code tcl> | <code tcl> | ||
- | source " | + | vmd> |
</ | </ | ||
You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions> | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions> | ||
- | * Now using " | + | * Now using " |
+ | - Go to Graphics > Labels | ||
+ | - In the drop-down list chose Dihedrals | ||
+ | - Chose both dihedrals in the list | ||
+ | - Go to the " | ||
+ | - Press on the "Graph..." button | ||
+ | - (Optional) save these graps in a text file (File > Export to ASCII matrix...) | ||
<note tip> | <note tip> |
exercises/2015_ethz_mmm/md_ala.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1