exercises:2014_ethz_mmm:alanine_modify
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exercise:alanine_modify [2014/03/06 10:31] – dpasserone | exercise:2014_ethz_mmm:alanine_modify [2014/10/15 13:28] – oschuett | ||
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====== Modification of the dihedral parameters ====== | ====== Modification of the dihedral parameters ====== | ||
- | <note important> | + | <note important> |
The relevant files are: | The relevant files are: | ||
- For the non-restrained optimizations to get A and B configurations, | - For the non-restrained optimizations to get A and B configurations, | ||
- For the restrained optimization along a chain, line_ij and inp_ff.templ, | - For the restrained optimization along a chain, line_ij and inp_ff.templ, | ||
- | - For the line simulation with the dihedral parameters modified, (from 1x to 6x) | + | - 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, | + | - 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 | ||
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- Check the final energies (grep 'E =' b_opt-pos-1.pdb ) | - Check the final energies (grep 'E =' b_opt-pos-1.pdb ) | ||
- copy the optimized a configuration into aopt.pdb. | - copy the optimized a configuration into aopt.pdb. | ||
- | - 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 | + | - Substitute the values of the angles in the line_ij |
- | - In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?) | + | - <note important> |
- | - 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? | + | - 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 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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1