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exercises:2015_ethz_mmm:alanine_modify [2015/02/27 08:02] – 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
Line 18: Line 23:
  
 <note important> <note important>
- 
- 
 The relevant files are: The relevant files are:
   - For the non-restrained optimizations to get A and B configurations, inp.a and inp.b   - For the non-restrained optimizations to get A and B configurations, inp.a and inp.b
-  - For the restrained optimization along a chain, ff_unchanged and inp_ff.templ, respectively the script to generate the "path" and the input file model for cp2k. +  - For the restrained optimization along a chain, ff_modify and inp_ff.templ, respectively the script to generate the "path" and the input file model for cp2k. 
-  - For the line simulation with the dihedral parameters modified, (from 1x to 4x), ff_multiply and ff_divide.  +  - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_modify.
-  - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_multiply and ff_divide.+
 </note> </note>
 +
 In this exercise, you are requested to start from the results of exercise 2, and perform the following steps In this exercise, you are requested to start from the results of exercise 2, and perform the following steps
  
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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>
 +
 +
 +
 +
 The input file inp.a is similar to the one of exercise 2.2, but the "constraint" part was removed to perform a "free" geometry optimization. An important line is the initial configuration filename: ini.a.pdb  The input file inp.a is similar to the one of exercise 2.2, but the "constraint" part was removed to perform a "free" geometry optimization. An important line is the initial configuration filename: ini.a.pdb 
-Copy the opt.1.3.pdb into Minimum_a/ini.a.pdb. +Copy the opt.1.3.pdb into ini.a.pdb. 
  
  
 Run cp2k with: Run cp2k with:
 <code bash> <code bash>
-you@eulerX Minimum_a$ 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 Minimum_a$ 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 psi and phi angles **using the script m_pdbtorsion**, in the file amin.pdb. Note these angles on a piece of paper. Check the final psi and phi angles **using the script m_pdbtorsion**, in the file amin.pdb. Note these angles on a piece of paper.
  
-Go to the Minimum_b folder and do the same with inp.b (but now use opt.3.2.pdb as a starting point, not opt.1.3.pdb) , run cp2k in a similar way, and measure both torsion angles in the file bmin.pdb, **that you may obtain using the "tail" command as before**.+Do the same with inp.b (but now use opt.3.2.pdb as a starting point, not opt.1.3.pdb) , run cp2k in a similar way, and measure both torsion angles in the file bmin.pdb, **that you may obtain using the "tail" command as before**.
  
 <note tip>  <note tip> 
 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?
 </note> </note>
  
-Now go to the "Line_nochange" folder and  copy the optimized "a" configuration into "ini.pdb". +Now copy the optimized "a" configuration into "ini.pdb". 
-Substitute the values of the angles in the **ff_unchanged** script:+Substitute the values of the angles in the **ff_modify** script:
 <code bash> <code bash>
 PHI_A="some_value" PHI_A="some_value"
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 and submit a new job: and submit a new job:
 <code> <code>
-you@eulerX Line_nochange$ bsub < ff_unchanged+you@eulerX exercise_2.3$ bsub < ff_modify
 </code>  </code> 
-which will generate a line (again using restraints to fix the dihedrals along this line). Again, this time you will have an output line with three columns (file eneline): 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.
 <note important>  <note important> 
 1 Hartree=27.2116 eV=627.509 kcal/mol 1 Hartree=27.2116 eV=627.509 kcal/mol
 </note>  </note> 
-In this way you will obtain an energy profile joining the two minima +In this way you will obtain energy profiles joining the two minima  
 +<note tip> 
 +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> <note tip>
-Would it be an idea to do a nudged elastic band?+How will the line profile change? Why?
 </note> </note>
-  - Now, you can create a new directory, and use a different potential file where a dihedral angle is increased or decreased. This task is performed by the **ff_multiply** script file, where you need again to substitute the values of the A and B pairs of angles to interpolate. 
-  - This time different enemol* files will be generated, each for a modified strength of the bond parameters.  
-  - Similarly, the **ff_divide** will generate profiles with the strength divided by 2,4... in the files **enediv.2, enediv.4**... 
-  - 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.1425024173.txt.gz · Last modified: 2020/08/21 10:14 (external edit)