User Tools

Site Tools


exercises:2015_ethz_mmm:alanine_modify

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
exercises:2015_ethz_mmm:alanine_modify [2015/02/27 08:07] dpasseroneexercises:2015_ethz_mmm:alanine_modify [2020/08/21 10:15] (current) – external edit 127.0.0.1
Line 1: Line 1:
 ====== 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>
  
Line 34: Line 36:
 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> 
-<note warning>We will structure our work a bit more here. We have 5 tasks, for each of them we will create a subdirectory: +HintDefinition of **PHI** and **PSI** torsion angles for this particular system is the following... 
-  - Optimization of first minimum --> mkdir Minimum_a +<code bash
-  - Optimization of second minimum --mkdir Minimum_b +PHI: 5 7 9 15 
-  - Energy profile along a line, original force field --> mkdir Line_nochange +PSI: 7 9 15 17 
-  - Energy profile along a line, enhanced force field --> mkdir Line_multiply +</code>
-  - Energy profile along a line, reduced force field --mkdir Line_divide +
-It is now your task to copy the necessary files (input, potential, initial configurations) into the correct directories. Most probably if a file is forgotten, your **cp2k** job will not work or give an error. +
 </note> </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>
  
Line 69: Line 72:
 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"
Line 90: Line 93:
 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)Againthis 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 0.250.5, 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.1425024459.txt.gz · Last modified: 2020/08/21 10:14 (external edit)