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exercises:2015_ethz_mmm:alanine_modify [2015/02/26 16:54] yakutovichexercises: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 12: Line 17:
  
 Go to the directory “exercise_2.3/ Go to the directory “exercise_2.3/
-<code>+<code bash>
 you@eulerX ~$ cd exercise_2.3 you@eulerX ~$ cd exercise_2.3
 </code> </code>
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, line_ij 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 6x), ff_multiply_ij and ff_divide_ij.  +  - 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_ij and ff_divide_ij.+
 </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
  
-  - Choose  two configurations A and B from the previously optimized grid (you can find them in the folder ~/exercise_2.2/Logs), close to the two minima. I suggest opt.1.4.pdb and opt.3.1.pdb. +Choose  two configurations A and B from the previously optimized grid (you can find them in the folder ~/exercise_2.2/Logs), close to the two minima. I suggest opt.1.3.pdb and opt.3.2.pdb.  
 <note> <note>
-Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory: +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 measure the dihedral angles, use the key "4" when focused on the vmd GUI, and select the appropriate atoms (see the definition of the dihedral in the file inp.templ of the previous exercise. This first measurement is only a check. +To get help how to use the program simply type its name without any argument, and press "Enter": 
-  - The input file inp.a is similar to the one of exercise 2.2, but I removed the "constraintpart so to perform a "free" geometry optimization +<code> 
-  - An important line is the initial configuration filenameini.a.pdb  +you@eulerX exercise_2.3$ m_pdbtorsion 
-  - Copy the opt.1.4.pdb into ini.a.pdb.  +</code>
-  - Run cp2k with  +
-<note tip>bsub cp2k.popt -i inp.a > out.a </note>+
  
-  - Check with vmd the final psi and phi angles, in the file a_opt-pos-1.pdb. Note these angles on a piece of paper. +<note> 
-  Do the same with inp.b, run the code in a similar way, and measure the b angles b_opt-pos-1.pdb. +Hint: Definition of **PHI** and **PSI** torsion angles for this particular system is the following... 
-  Check the final energies (grep 'E =' b_opt-pos-1.pdb ) +<code bash> 
-  - copy the optimized a configuration into aopt.pdb. +PHI: 5 7 9 15 
-  Substitute the values of the angles in the line_ij scriptand generate 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. +PSI: 7 9 15 17 
-  <note important>1 Hartree=27.2116 eV=627.509 kcal/mol</note>  +</code> 
-  In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?). +</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_ij** script file, where you need again to substitute the values of the A and B pairs of angles to interpolate. + 
-  - This time different enemolfiles will be generated, each for a modified strength of the bond parameters.  + 
-  - Similarly, the **ff_divide_ij** will generate profiles with the strength divided by 2,3,4... in the files **enediv.2, enediv.3, enediv.4**... + 
-  The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential.  + 
-  How will the line profile change? Why?+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 ini.a.pdb.  
 + 
 + 
 +Run cp2k with: 
 +<code bash> 
 +you@eulerX exercise_2.3$ bsub cp2k.popt -i inp.a -o out.a  
 +</code> 
 + 
 +The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one: 
 +<code bash> 
 +you@eulerX exercise_2.3$ tail -25  a_opt-pos-1.pdb > amin.pdb 
 +</code> 
 + 
 +meaning that you get the "tail" of the file (last 25 lines) and you put these lines in the file amin.pdb. 
 +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. 
 + 
 +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>  
 +Check the final energies
 +<code bash> 
 +you@eulerX exercise_2.3$ grep 'E =' a_opt-pos-1.pdb 
 +you@eulerX exercise_2.3$ grep 'E =' b_opt-pos-1.pdb 
 +</code> 
 +Is the energy becoming lower during the optimization? 
 +</note> 
 + 
 +Now copy the optimized "aconfiguration into "ini.pdb"
 +Substitute the values of the angles in the **ff_modify** script
 +<code bash> 
 +PHI_A="some_value" 
 +PHI_B="some_value" 
 +PSI_A="some_value" 
 +PSI_B="some_value" 
 +</code> 
 +and submit new job: 
 +<code> 
 +you@eulerX exercise_2.3$ bsub < ff_modify 
 +</code>  
 +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>  
 +1 Hartree=27.2116 eV=627.509 kcal/mol 
 +</note>  
 +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> 
 +How will the line profile change? Why? 
 +</note>
exercises/2015_ethz_mmm/alanine_modify.1424969672.txt.gz · Last modified: 2020/08/21 10:14 (external edit)