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exercises:2017_ethz_mmm:alanine_modify [2017/02/22 10:01] (current)
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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
 +</​note>​
  
 +
 +Download the 2.3 exercise into your $HOME folder and unzip it.
 +<code bash>
 +you@eulerX ~$ wget http://​www.cp2k.org/​_media/​exercises:​2015_ethz_mmm:​exercise_2.3.zip
 +you@eulerX ~$ unzip exercises:​2015_ethz_mmm:​exercise_2.3.zip
 +</​code>​
 +
 +<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}}</​note>​
 +
 +
 +
 +Go to the directory “exercise_2.3/​”
 +<code bash>
 +you@eulerX ~$ cd exercise_2.3
 +</​code>​
 +
 +
 +<note important>​
 +The relevant files are:
 +  - For the non-restrained optimizations to get A and B configurations,​ inp.a and inp.b
 +  - For the restrained optimization along a chain, ff_modify and inp_ff.templ,​ respectively the script to generate the "​path"​ and the input file model for cp2k.
 +  - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ,​ that will be used by ff_modify.
 +</​note>​
 +
 +In this exercise, you are requested to start from the results of exercise 2, and perform the following steps
 +
 +Choose ​ two configurations A and B from the previously optimized grid (you can find them in the folder ~/​exercise_2.2/​Logs),​ close to the two minima. I suggest opt.1.3.pdb and opt.3.2.pdb. ​
 +
 +<​note>​
 +Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: ​
 +<​code>​
 +you@eulerX exercise_2.3$ . ~/​Scripts/​myfunctions.bash
 +</​code>​
 +</​note>​
 +To get help how to use the program simply type its name without any argument, and press "​Enter":​
 +<​code>​
 +you@eulerX exercise_2.3$ m_pdbtorsion
 +</​code>​
 +
 +<​note>​
 +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
 +</​code>​
 +</​note>​
 +
 +
 +
 +
 +The input file inp.a is similar to the one of exercise 2.2, but the "​constraint"​ part was removed to perform a "​free"​ geometry optimization. An important line is the initial configuration filename: ini.a.pdb ​
 +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 
 +</​code>​
 +
 +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
 +</​code>​
 +
 +meaning that you get the "​tail"​ of the file (last 25 lines) and you put these lines in the file amin.pdb.
 +Check the final psi and phi angles **using the script m_pdbtorsion**,​ in the file amin.pdb. Note these angles on a piece of paper.
 +
 +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 "​tail"​ command as before**.
 +
 +<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
 +</​code>​
 +Is the energy becoming lower during the optimization?​
 +</​note>​
 +
 +Now copy the optimized "​a"​ configuration into "​ini.pdb"​.
 +Substitute the values of the angles in the **ff_modify** script:
 +<code bash>
 +PHI_A="​some_value"​
 +PHI_B="​some_value"​
 +PSI_A="​some_value"​
 +PSI_B="​some_value"​
 +</​code>​
 +and submit a new job:
 +<​code>​
 +you@eulerX exercise_2.3$ bsub < ff_modify
 +</​code> ​
 +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.* ​ with three columns : the restrained phi, psi, and the energy in Hartree.
 +<note important> ​
 +1 Hartree=27.2116 eV=627.509 kcal/mol
 +</​note> ​
 +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?
 +</​note>​
 +  * The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load "​mod_ff.gnu"​ from within gnuplot:
 +<code gnuplot>
 +you@eulerX exercise_2.3$ gnuplot
 +gnuplot> load "​mod_ff.gnu"​
 +</​code>​
 +<note tip>
 +How will the line profile change? Why?
 +</​note>​
exercises/2017_ethz_mmm/alanine_modify.txt · Last modified: 2017/02/22 10:01 (external edit)