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exercises:2014_ethz_mmm:alanine_modify

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Modification of the dihedral parameters

The files for this exercise are in /cluster/home03/matl/danielep/LECTURE2/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)
  4. For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_ij.

In this exercise, you are requested to start from the results of exercise 2, and perform the following steps

  1. 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.
  2. 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.
  3. 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
  4. An important line is the initial configuration filename: ini.a.pdb
  5. Copy the opt.1.4.pdb into ini.a.pdb.
  6. Run cp2k with
bsub cp2k.popt -i inp.a > out.a
  1. 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.
  2. Do the same with inp.b, run the code in a similar way, and measure the b angles b_opt-pos-1.pdb.
  3. Check the final energies (grep 'E =' b_opt-pos-1.pdb )
  4. copy the optimized a configuration into aopt.pdb.
  5. Substitute the values of the angles in the ff_ij script, and generate a line (again using restraints to fix the dihedrals along this line). Again, this time you will have a
  6. In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?)
  7. Now, you can create a new directory, and use a different potential file where a dihedral angle is increased or decreased. How will the line profile change? Why?
exercises/2014_ethz_mmm/alanine_modify.1394101913.txt.gz · Last modified: 2014/03/06 10:31 by dpasserone