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
- Choose (use vmd to measure the angles) two configurations A and B from the previously optimized grid, close to the two minima
- Remove the “restraint” part and perform a “free” geometry optimization
- once the two optimum geometries are obtained, open the two optimized configurations with vmd and mark the two angles
- Substitute the values of the angles in the following script, and generate a line (again using restraints to fix the dihedrals along this line)
- 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. How will the line profile change? Why?
exercises/2014_ethz_mmm/alanine_modify.1393420435.txt.gz · Last modified: 2020/08/21 10:14 (external edit)