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exercises:2015_ethz_mmm:alanine_modify

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Modification of the dihedral parameters

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
All files of this exercise ( input and scripts are all commented ) can be downloaded from the wiki: exercise_2.3.zip

Go to the directory “exercise_2.3/”

you@eulerX ~$ cd exercise_2.3
The relevant files are:
  1. For the non-restrained optimizations to get A and B configurations, inp.a and inp.b
  2. 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.
  3. For the line simulation with the dihedral parameters modified, (from 1x to 4x), ff_multiply and ff_divide.
  4. For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_multiply and ff_divide.

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.

Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first:
you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash

To get help how to use the program simply type its name without any argument, and press “Enter”

you@eulerX exercise_2.3$ m_pdbtorsion

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.

Run cp2k with:

you@eulerX Minimum_a$ bsub cp2k.popt -i inp.a -o out.a 

The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one:

you@eulerX Minimum_a$ tail -25  a_opt-pos-1.pdb > amin.pdb

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.

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.

Check the final energies:
you@eulerX Minimum_a$ grep 'E =' a_opt-pos-1.pdb
you@eulerX Minimum_b$ grep 'E =' b_opt-pos-1.pdb

Is the energy becoming lower during the optimization?

Now go to the “Line_nochange” folder and copy the optimized “a” configuration into “ini.pdb”. Substitute the values of the angles in the ff_unchanged script:

PHI_A="some_value"
PHI_B="some_value"
PSI_A="some_value"
PSI_B="some_value"

and submit a new job:

you@eulerX Line_nochange$ bsub < ff_unchanged

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.

1 Hartree=27.2116 eV=627.509 kcal/mol

In this way you will obtain an energy profile joining the two minima

Would it be an idea to do a nudged elastic band?
  1. 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.
  2. This time different enemol* files will be generated, each for a modified strength of the bond parameters.
  3. Similarly, the ff_divide will generate profiles with the strength divided by 2,4… in the files enediv.2, enediv.4
  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.
  5. 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)