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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

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
  2. Remove the “restraint” part and perform a “free” geometry optimization
  3. once the two optimum geometries are obtained, open the two optimized configurations with vmd and mark the two angles
  4. Substitute the values of the angles in the following script, and generate a line (again using restraints to fix the dihedrals along this line)
  5. In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?)
  6. 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.1393420435.txt.gz · Last modified: 2014/02/26 13:13 by dpasserone