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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
Go to the directory “exercise_2.3/”
you@eulerX ~$ cd exercise_2.3
- 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 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_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.1.3.pdb and opt.3.2.pdb.
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, 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.
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.
In this way you will obtain an energy profile joining the two minima
- 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?