exercises:2015_ethz_mmm:alanine_modify
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exercises:2015_ethz_mmm:alanine_modify [2015/02/27 09:10] – yakutovich | exercises:2015_ethz_mmm:alanine_modify [2015/03/06 02:40] – dpasserone | ||
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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. | Download the 2.3 exercise into your $HOME folder and unzip it. | ||
Line 31: | Line 36: | ||
Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: | Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first: | ||
< | < | ||
- | you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash | + | you@eulerX exercise_2.3$ . ~/Scripts/myfunctions.bash |
</ | </ | ||
</ | </ | ||
- | To get help how to use the program simply type its name without any argument, and press " | + | To get help how to use the program simply type its name without any argument, and press " |
< | < | ||
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 | ||
+ | </ | ||
+ | </ | ||
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In this way you will obtain energy profiles joining the two minima | In this way you will obtain energy profiles joining the two minima | ||
<note tip> | <note tip> | ||
- | Would it be an idea to do a nudged elastic band? | + | Could you expain |
</ | </ | ||
- | | + | |
- | | + | <code gnuplot> |
+ | you@eulerX exercise_2.3$ gnuplot | ||
+ | gnuplot> load " | ||
+ | </ | ||
+ | |
exercises/2015_ethz_mmm/alanine_modify.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1