The commented files for this exercise can be downloaded from the wiki: exercise_2.3.zip
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, 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 (use vmd to measure the angles) two configurations A and B from the previously optimized grid, close to the two minima. I suggest opt.1.4.pdb and opt.3.1.pdb.
To measure the dihedral angles, use the key “4” when focused on the vmd GUI, and select the appropriate atoms (see the definition of the dihedral in the file inp.templ of the previous exercise. This first measurement is only a check.
The input file inp.a is similar to the one of exercise 2.2, but I removed the “constraint” part so to perform a “free” geometry optimization
An important line is the initial configuration filename: ini.a.pdb
Copy the opt.1.4.pdb into ini.a.pdb.
Run cp2k with
bsub cp2k.popt -i inp.a > out.a
Check with vmd the final psi and phi angles, in the file a_opt-pos-1.pdb. Note these angles on a piece of paper.
Do the same with inp.b, run the code in a similar way, and measure the b angles b_opt-pos-1.pdb.
Check the final energies (grep 'E =' b_opt-pos-1.pdb )
copy the optimized a configuration into aopt.pdb.
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.
In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?).
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.
This time different enemol* files will be generated, each for a modified strength of the bond parameters.
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…
The mod_ff.gnu file will plot all that, and the shape of the harmonic dihedral potential.
How will the line profile change? Why?
exercises/2014_ethz_mmm/alanine_modify.1402355652.txt.gz · Last modified: 2014/06/09 23:14 by dpasserone