exercises:2015_ethz_mmm:alanine_modify
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exercises:2015_ethz_mmm:alanine_modify [2015/02/26 23:41] – dpasserone | exercises:2015_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 warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | you@eulerX ~$ module load courses mmm ; mmm-init | ||
+ | </ | ||
+ | Download the 2.3 exercise into your $HOME folder and unzip it. | ||
<code bash> | <code bash> | ||
you@eulerX ~$ wget http:// | you@eulerX ~$ wget http:// | ||
Line 18: | Line 23: | ||
<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, | + | - For the restrained optimization along a chain, |
- | - 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 | ||
Line 33: | Line 36: | ||
Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: | Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: | ||
< | < | ||
- | you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash | + | you@eulerX exercise_2.3$ . ~/Scripts/myfunctions.bash |
</ | </ | ||
</ | </ | ||
- | To get help how to use the program simply type its name without any argument, and press " | + | To get help how to use the program simply type its name without any argument, and press " |
< | < | ||
you@eulerX exercise_2.3$ m_pdbtorsion | you@eulerX exercise_2.3$ m_pdbtorsion | ||
</ | </ | ||
+ | |||
+ | < | ||
+ | Hint: Definition of **PHI** and **PSI** torsion angles for this particular system is the following... | ||
+ | <code bash> | ||
+ | PHI: 5 7 9 15 | ||
+ | PSI: 7 9 15 17 | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | |||
The input file inp.a is similar to the one of exercise 2.2, but the " | The input file inp.a is similar to the one of exercise 2.2, but the " | ||
- | Copy the opt.1.3.pdb into Minimum_a/ini.a.pdb. | + | Copy the opt.1.3.pdb into ini.a.pdb. |
Run cp2k with: | Run cp2k with: | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
</ | </ | ||
The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one: | The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one: | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
</ | </ | ||
meaning that you get the " | meaning that you get the " | ||
- | Check the final psi and phi angles, in the file amin.pdb. Note these angles on a piece of paper. | + | Check the final psi and phi angles |
- | Go to the Minimum_b folder and do the same with inp.b (but now use opt.3.2.pdb as a starting point, not opt.1.3.pdb) , run cp2k in a similar way, and measure both torsion angles in the file bmin.pdb, that you may obtain using the " | + | Do the same with inp.b (but now use opt.3.2.pdb as a starting point, not opt.1.3.pdb) , run cp2k in a similar way, and measure both torsion angles in the file bmin.pdb, |
<note tip> | <note tip> | ||
Check the final energies: | Check the final energies: | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
</ | </ | ||
Is the energy becoming lower during the optimization? | Is the energy becoming lower during the optimization? | ||
</ | </ | ||
- | Now go to the " | + | Now copy the optimized " |
- | Substitute the values of the angles in the **ff_unchanged** script: | + | Substitute the values of the angles in the **ff_modify** script: |
<code bash> | <code bash> | ||
PHI_A=" | PHI_A=" | ||
Line 78: | Line 93: | ||
and submit a new job: | and submit a new job: | ||
< | < | ||
- | you@eulerX | + | you@eulerX |
</ | </ | ||
- | which will generate a line (again using restraints to fix the dihedrals along this line). Again, this time you will have an output | + | which will perform different jobs with the torsional term for the angle **PSI** modified by multiplication by 0.25, 0.5, 1, 2, 4. This corresponds to output |
<note important> | <note important> | ||
1 Hartree=27.2116 eV=627.509 kcal/mol | 1 Hartree=27.2116 eV=627.509 kcal/mol | ||
</ | </ | ||
- | In this way you will obtain | + | In this way you will obtain energy |
+ | <note tip> | ||
+ | Could you expain an idea how to setup a nudged elastic band simulation to study the reaction pathway from **A** to the **B** point? | ||
+ | </ | ||
+ | * The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load " | ||
+ | <code gnuplot> | ||
+ | you@eulerX exercise_2.3$ gnuplot | ||
+ | gnuplot> load " | ||
+ | </ | ||
<note tip> | <note tip> | ||
- | Would it be an idea to do a nudged elastic band? | + | How will the line profile change? Why? |
</ | </ | ||
- | - 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** 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** will generate profiles with the strength divided by 2,4... in the files **enediv.2, enediv.4**... | ||
- | - The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load " | ||
- | - How will the line profile change? Why? |
exercises/2015_ethz_mmm/alanine_modify.1424994090.txt.gz · Last modified: 2020/08/21 10:14 (external edit)