====== 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 $HOME folder and unzip it.
<code bash>
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.3.zip
you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.3.zip
</code>

<note tip> All files of this exercise (** input and scripts are all commented **) can be downloaded from the wiki: {{exercise_2.3.zip|exercise_2.3.zip}}</note>



Go to the directory “exercise_2.3/”
<code bash>
you@eulerX ~$ cd exercise_2.3
</code>


<note important>
The relevant files are:
  - For the non-restrained optimizations to get A and B configurations, inp.a and inp.b
  - 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 potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_modify.
</note>

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.1.3.pdb and opt.3.2.pdb. 

<note>
Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: 
<code>
you@eulerX exercise_2.3$ . ~/Scripts/myfunctions.bash
</code>
</note>
To get help how to use the program simply type its name without any argument, and press "Enter":
<code>
you@eulerX exercise_2.3$ m_pdbtorsion
</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 
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 "a" configuration 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 a 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 0.25, 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> 
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>