exercises:2014_ethz_mmm:alanine_modify
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exercise:alanine_modify [2014/02/28 08:14] – dpasserone | exercises:2014_ethz_mmm:alanine_modify [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Modification of the dihedral parameters ====== | ====== Modification of the dihedral parameters ====== | ||
- | <note important> | + | <note important> |
- | The relevant files are ff_ij and inp_ff.templ, | + | The relevant files are: |
+ | - For the non-restrained optimizations to get A and B configurations, | ||
+ | - For the restrained optimization along a chain, line_ij | ||
+ | - 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, | ||
</ | </ | ||
In this exercise, you are requested to start from the results of exercise 2, and perform the following steps | 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 | + | - 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. |
- | - Remove | + | - To measure |
- | - once the two optimum geometries are obtained, open the two optimized configurations with vmd and mark the two angles | + | - The input file inp.a is similar to the one of exercise 2.2, but I removed the " |
- | - Substitute | + | - An important line is the initial configuration filename: ini.a.pdb |
- | - In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?) | + | - Copy the opt.1.4.pdb into ini.a.pdb. |
- | - Now, you can create | + | - Run cp2k with |
+ | <note tip>bsub cp2k.popt | ||
+ | - 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. | ||
+ | - <note important> | ||
+ | - 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.1393575261.txt.gz · Last modified: 2020/08/21 10:14 (external edit)