# Open SourceMolecular Dynamics

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exercises:2017_ethz_mmm:alanine_modify

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 — exercises:2017_ethz_mmm:alanine_modify [2017/02/22 10:01] (current) Line 1: Line 1: + ====== Modification of the dihedral parameters ====== + + 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. + + 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 + ​ + + 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/​” + + you@eulerX ~$cd exercise_2.3 + ​ + + + ​ + The relevant files are: + - For the non-restrained optimizations to get A and B configurations,​ inp.a and inp.b + - For the restrained optimization along a chain, ff_modify and inp_ff.templ,​ respectively the script to generate the "​path"​ and the input file model for cp2k. + - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ,​ that will be used by ff_modify. + ​ + + In this exercise, you are requested to start from the results of exercise 2, and perform the following steps + + Choose ​ two configurations A and B from the previously optimized grid (you can find them in the folder ~/​exercise_2.2/​Logs),​ close to the two minima. I suggest opt.1.3.pdb and opt.3.2.pdb. ​ + + <​note>​ + Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: ​ + <​code>​ + you@eulerX exercise_2.3$ . ~/​Scripts/​myfunctions.bash + ​ + ​ + To get help how to use the program simply type its name without any argument, and press "​Enter":​ + <​code>​ + you@eulerX exercise_2.3$m_pdbtorsion + ​ + + <​note>​ + Hint: Definition of **PHI** and **PSI** torsion angles for this particular system is the following... + + PHI: 5 7 9 15 + PSI: 7 9 15 17 + ​ + ​ + + + + + The input file inp.a is similar to the one of exercise 2.2, but the "​constraint"​ part was removed to perform a "​free"​ geometry optimization. An important line is the initial configuration filename: ini.a.pdb ​ + Copy the opt.1.3.pdb into ini.a.pdb. ​ + + + Run cp2k with: + + you@eulerX exercise_2.3$ 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: + + you@eulerX exercise_2.3$tail -25 a_opt-pos-1.pdb > amin.pdb + ​ + + meaning that you get the "​tail"​ of the file (last 25 lines) and you put these lines in the file amin.pdb. + Check the final psi and phi angles **using the script m_pdbtorsion**,​ in the file amin.pdb. Note these angles on a piece of paper. + + Do the same with inp.b (but now use opt.3.2.pdb as a starting point, not opt.1.3.pdb) , run cp2k in a similar way, and measure both torsion angles in the file bmin.pdb, **that you may obtain using the "​tail"​ command as before**. + + ​ + Check the final energies: + + you@eulerX exercise_2.3$ grep 'E =' a_opt-pos-1.pdb + you@eulerX exercise_2.3$grep 'E =' b_opt-pos-1.pdb + ​ + Is the energy becoming lower during the optimization?​ + ​ + + Now copy the optimized "​a"​ configuration into "​ini.pdb"​. + Substitute the values of the angles in the **ff_modify** script: + + PHI_A="​some_value"​ + PHI_B="​some_value"​ + PSI_A="​some_value"​ + PSI_B="​some_value"​ + ​ + and submit a new job: + <​code>​ + you@eulerX exercise_2.3$ 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.* ​ with three columns : the restrained phi, psi, and the energy in Hartree. +  ​ + 1 Hartree=27.2116 eV=627.509 kcal/mol +  ​ + In this way you will obtain energy profiles joining the two minima ​ + + 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 "​mod_ff.gnu"​ from within gnuplot: + + you@eulerX exercise_2.3\$ gnuplot + gnuplot> load "​mod_ff.gnu"​ + ​ + + How will the line profile change? Why? +
exercises/2017_ethz_mmm/alanine_modify.txt · Last modified: 2017/02/22 10:01 (external edit)