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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, line_ij 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 6x), ff_multiply_ij and ff_divide_ij.
  4. 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.

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.

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 withot 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.1.4.pdb into Minimum_a/ini.a.pdb.

Run cp2k with:

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

Check the final psi and phi angles, in the file a_opt-pos-1.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.3.1.pdb as a starting point, not opt.1.4.pdb) , run cp2k in a similar way, and measure both torsion angles in the file b_opt-pos-1.pdb.

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?

Copy the optimized a configuration into aopt.pdb.

  1. Substitute the values of the angles in the line_ij script, and 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
  1. In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?).
  2. 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.
  3. This time different enemol* files will be generated, each for a modified strength of the bond parameters.
  4. 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
  5. The mod_ff.gnu file will plot all that, and the shape of the harmonic dihedral potential.
  6. How will the line profile change? Why?
exercises/2015_ethz_mmm/alanine_modify.1424985240.txt.gz · Last modified: 2020/08/21 10:14 (external edit)