exercises:2017_ethz_mmm:alanine_modify
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— | exercises:2017_ethz_mmm:alanine_modify [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== 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 $HOME folder and unzip it. | ||
+ | <code bash> | ||
+ | you@eulerX ~$ wget http:// | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | </ | ||
+ | |||
+ | <note tip> All files of this exercise (** input and scripts are all commented **) can be downloaded from the wiki: {{exercise_2.3.zip|exercise_2.3.zip}}</ | ||
+ | |||
+ | |||
+ | |||
+ | Go to the directory “exercise_2.3/ | ||
+ | <code bash> | ||
+ | you@eulerX ~$ cd exercise_2.3 | ||
+ | </ | ||
+ | |||
+ | |||
+ | <note important> | ||
+ | The relevant files are: | ||
+ | - For the non-restrained optimizations to get A and B configurations, | ||
+ | - For the restrained optimization along a chain, ff_modify and inp_ff.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 | ||
+ | |||
+ | Choose | ||
+ | |||
+ | < | ||
+ | Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: | ||
+ | < | ||
+ | you@eulerX exercise_2.3$ . ~/ | ||
+ | </ | ||
+ | </ | ||
+ | To get help how to use the program simply type its name without any argument, and press " | ||
+ | < | ||
+ | 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 " | ||
+ | Copy the opt.1.3.pdb into ini.a.pdb. | ||
+ | |||
+ | |||
+ | Run cp2k with: | ||
+ | <code bash> | ||
+ | you@eulerX exercise_2.3$ bsub cp2k.popt -i inp.a -o out.a | ||
+ | </ | ||
+ | |||
+ | The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one: | ||
+ | <code bash> | ||
+ | you@eulerX exercise_2.3$ tail -25 a_opt-pos-1.pdb > amin.pdb | ||
+ | </ | ||
+ | |||
+ | meaning that you get the " | ||
+ | Check the final psi and phi angles **using the script m_pdbtorsion**, | ||
+ | |||
+ | 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> | ||
+ | Check the final energies: | ||
+ | <code bash> | ||
+ | you@eulerX exercise_2.3$ grep 'E =' a_opt-pos-1.pdb | ||
+ | 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** script: | ||
+ | <code bash> | ||
+ | PHI_A=" | ||
+ | PHI_B=" | ||
+ | PSI_A=" | ||
+ | PSI_B=" | ||
+ | </ | ||
+ | and submit a new job: | ||
+ | < | ||
+ | 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 lines enemul.* | ||
+ | <note important> | ||
+ | 1 Hartree=27.2116 eV=627.509 kcal/mol | ||
+ | </ | ||
+ | In this way you will obtain energy profiles joining the two minima | ||
+ | <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> | ||
+ | How will the line profile change? Why? | ||
+ | </ |
exercises/2017_ethz_mmm/alanine_modify.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1