Differences

This shows you the differences between two versions of the page.

@@ Line 1: / Line 1: @@
+====== 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>
+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>