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exercises:2015_ethz_mmm:md_ala

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exercises:2015_ethz_mmm:md_ala [2015/03/11 10:33] – yakutovichexercises: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
 </note> </note>
  
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 </code> </code>
  
 +<note tip>
 +To get more information, please visit **cp2k reference manual**, section **Molecular Dynamics**:
 +http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html
 +</note>
  
   * 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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 </code> </code>
  
-Edit the inp.100 file (Put there: NPT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K: +Edit the inp.100 file (Put there: NVT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K: 
 <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 "dihedrals.vmd"+vmd> source "dihedrals.vmd"
 </code> </code>
  
 You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions>Analysis>RMSC Trajectory Tool). Replace the word "protein" with "all" in the selection, and then use "align". You will see that now the molecule is well aligned along the path. You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions>Analysis>RMSC Trajectory Tool). Replace the word "protein" with "all" in the selection, and then use "align". You will see that now the molecule is well aligned along the path.
  
-  * Now using "Labels" menu, plot the graph of two dihedral angles.+  * Now using "Labels" menu, plot the graph of two dihedral angles: 
 +  - Go to Graphics > Labels 
 +  - In the drop-down list chose Dihedrals 
 +  - Chose both dihedrals in the list 
 +  - Go to the "Graph" section 
 +  - 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.1426070037.txt.gz · Last modified: (external edit)