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exercises:2015_ethz_mmm:alanine_modify [2015/02/27 08:41] – dpasseroneexercises:2015_ethz_mmm:alanine_modify [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ====== Modification of the dihedral parameters ====== ====== Modification of the dihedral parameters ======
 +<note warning>
 +TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
 +you@eulerX ~$ module load courses mmm ; mmm-init
 +</note>
  
  
 +Download the 2.3 exercise into your $HOME folder and unzip it.
 <code bash> <code bash>
 you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.3.zip you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.3.zip
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 Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first:  Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: 
 <code> <code>
-you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash+you@eulerX exercise_2.3$ . ~/Scripts/myfunctions.bash
 </code> </code>
 </note> </note>
-To get help how to use the program simply type its name without any argument, and press "Enter"+To get help how to use the program simply type its name without any argument, and press "Enter":
 <code> <code>
 you@eulerX exercise_2.3$ m_pdbtorsion you@eulerX exercise_2.3$ m_pdbtorsion
 </code> </code>
 +
 +<note>
 +Hint: Definition of **PHI** and **PSI** torsion angles for this particular system is the following...
 +<code bash>
 +PHI: 5 7 9 15
 +PSI: 7 9 15 17
 +</code>
 +</note>
  
  
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 Run cp2k with: Run cp2k with:
 <code bash> <code bash>
-you@eulerX $ bsub cp2k.popt -i inp.a -o out.a +you@eulerX exercise_2.3$ bsub cp2k.popt -i inp.a -o out.a 
 </code> </code>
  
 The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one: The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one:
 <code bash> <code bash>
-you@eulerX $ tail -25  a_opt-pos-1.pdb > amin.pdb+you@eulerX exercise_2.3$ tail -25  a_opt-pos-1.pdb > amin.pdb
 </code> </code>
  
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 Check the final energies: Check the final energies:
 <code bash> <code bash>
-you@eulerX Minimum_a$ grep 'E =' a_opt-pos-1.pdb +you@eulerX exercise_2.3$ grep 'E =' a_opt-pos-1.pdb 
-you@eulerX Minimum_b$ grep 'E =' b_opt-pos-1.pdb+you@eulerX exercise_2.3$ grep 'E =' b_opt-pos-1.pdb
 </code> </code>
 Is the energy becoming lower during the optimization? Is the energy becoming lower during the optimization?
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 and submit a new job: and submit a new job:
 <code> <code>
-you@eulerX $ bsub < ff_modify+you@eulerX exercise_2.3$ bsub < ff_modify
 </code>  </code> 
 which will perform different jobs with the torsional term for the angle **PSI** modified by multiplication by 0.25, 0.5, 1, 2, 4. This corresponds to output lines enemul.*  with three columns : the restrained phi, psi, and the energy in Hartree. which will perform different jobs with the torsional term for the angle **PSI** modified by multiplication by 0.25, 0.5, 1, 2, 4. This corresponds to output lines enemul.*  with three columns : the restrained phi, psi, and the energy in Hartree.
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 In this way you will obtain energy profiles joining the two minima  In this way you will obtain energy profiles joining the two minima 
 <note tip> <note tip>
-Would it be an idea to do a nudged elastic band?+Could you expain an idea how to setup a nudged elastic band simulation to study the reaction pathway from **A** to the **B** point? 
 +</note> 
 +  * The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load "mod_ff.gnu" from within gnuplot: 
 +<code gnuplot> 
 +you@eulerX exercise_2.3$ gnuplot 
 +gnuplot> load "mod_ff.gnu" 
 +</code> 
 +<note tip> 
 +How will the line profile change? Why?
 </note> </note>
-  - The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load "mod_ff.gnu" from within gnuplot. 
-  - How will the line profile change? Why? 
exercises/2015_ethz_mmm/alanine_modify.1425026490.txt.gz · Last modified: 2020/08/21 10:14 (external edit)