exercises:2015_ethz_mmm:alanine_modify
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exercises:2015_ethz_mmm:alanine_modify [2015/02/26 20:54] – yakutovich | 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 | ||
- | Choose | + | Choose |
< | < | ||
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 withot | + | To get help how to use the program simply type its name without |
< | < | ||
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.1.4.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 exercise_2.3$ | ||
+ | </ | ||
- | Check the final psi and phi angles, in the file a_opt-pos-1.pdb. Note these angles on a piece of paper. | + | The file a_opt-pos-1.pdb |
+ | <code bash> | ||
+ | you@eulerX exercise_2.3$ tail -25 a_opt-pos-1.pdb > amin.pdb | ||
+ | </ | ||
- | Go to the Minimum_b folder | + | meaning that you get the " |
- | | + | Check the final psi and phi angles **using the script m_pdbtorsion**, |
- | - copy the optimized a configuration into aopt.pdb. | + | |
- | | + | 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 " |
- | | + | |
- | | + | <note tip> |
- | - 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 | + | Check the final energies: |
- | - This time different enemol* files will be generated, each for a modified strength of the bond parameters. | + | <code bash> |
- | - 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**... | + | you@eulerX exercise_2.3$ |
- | | + | you@eulerX exercise_2.3$ grep 'E =' b_opt-pos-1.pdb |
- | | + | </ |
+ | Is the energy becoming lower during the optimization? | ||
+ | </ | ||
+ | |||
+ | Now copy the optimized | ||
+ | Substitute the values of the angles in the **ff_modify** | ||
+ | <code bash> | ||
+ | PHI_A=" | ||
+ | PHI_B=" | ||
+ | PSI_A=" | ||
+ | PSI_B=" | ||
+ | </ | ||
+ | and submit | ||
+ | < | ||
+ | you@eulerX exercise_2.3$ bsub < ff_modify | ||
+ | </ | ||
+ | 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> | ||
+ | 1 Hartree=27.2116 eV=627.509 kcal/mol | ||
+ | </ | ||
+ | In this way you will obtain energy | ||
+ | <note tip> | ||
+ | Could you expain | ||
+ | </ | ||
+ | | ||
+ | <code gnuplot> | ||
+ | you@eulerX exercise_2.3$ gnuplot | ||
+ | gnuplot> load " | ||
+ | </ | ||
+ | <note tip> | ||
+ | How will the line profile change? Why? | ||
+ | </ |
exercises/2015_ethz_mmm/alanine_modify.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1