Modification of the dihedral parameters
Download the 2.3 exercise into your $HOME folder and unzip it.
you@eulerX ~$ 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, 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.
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
PHI: 5 7 9 15 PSI: 7 9 15 17
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:
you@eulerX exercise_2.3$ 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 exercise_2.3$ 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.
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 exercise_2.3$ grep 'E =' a_opt-pos-1.pdb you@eulerX exercise_2.3$ grep 'E =' b_opt-pos-1.pdb
Is the energy becoming lower during the optimization?
Now copy the optimized “a” configuration into “ini.pdb”. Substitute the values of the angles in the ff_modify script:
PHI_A="some_value" PHI_B="some_value" PSI_A="some_value" PSI_B="some_value"
and submit a new job:
you@eulerX exercise_2.3$ bsub < ff_modify
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.
In this way you will obtain energy profiles joining the two minima
- 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:
you@eulerX exercise_2.3$ gnuplot gnuplot> load "mod_ff.gnu"