exercises:2015_ethz_mmm:alanine_dipeptide
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exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/06 17:49] – external edit 127.0.0.1 | exercises:2015_ethz_mmm:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Ramachandran plot for Alanine Dipeptide ====== | ====== Ramachandran plot for Alanine Dipeptide ====== | ||
+ | |||
+ | <note warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | you@eulerX ~$ module load courses mmm ; mmm-init | ||
+ | </ | ||
+ | |||
Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional angle Φ is C-N-C-C and Ψ is N-C-C-N along the backbone. | Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional angle Φ is C-N-C-C and Ψ is N-C-C-N along the backbone. | ||
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In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | ||
- | <note tip> | + | Download the 2.2 exercise into your $HOME folder and unzip it. |
+ | |||
+ | < | ||
+ | you@eulerX ~$ wget http:// | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | </ | ||
+ | |||
+ | <note tip> | ||
+ | Then go to the directory “exercise_2.2/ | ||
< | < | ||
- | you@brutusX ~$ mkdir mmm_exercise_2.2 | + | you@eulerX |
- | you@brutusX | + | |
- | you@brutusX mmm_exercise_2.2$ cp / | + | |
</ | </ | ||
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< | < | ||
- | you@brutusX mmm_exercise_2.2$ module load cp2k/ | + | you@eulerX exercise_2.2$ module load new cp2k |
- | you@brutusX mmm_exercise_2.2$ bsub < grid_brutus | + | you@eulerX exercise_2.2$ bsub < grid_alanine |
</ | </ | ||
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< | < | ||
- | you@brutusX mmm_exercise_2.2$ gnuplot | + | you@eulerX exercise_2.2$ gnuplot |
</ | </ | ||
+ | <note important> | ||
+ | Changing into the directory **Logs** you fill find files of the kind **opt.? | ||
+ | m_pdbtorsion: | ||
+ | < | ||
+ | you@eulerX exercise_2.2/ | ||
+ | </ | ||
+ | |||
+ | for the two dihedral **Phi** and **Psi**. | ||
+ | |||
+ | |||
+ | </ | ||
To clean the output and unnecessary files and do it again, | To clean the output and unnecessary files and do it again, | ||
< | < | ||
- | you@brutusX mmm_exercise_2.2$ ./cleanall | + | you@eulerX exercise_2.2$ ./cleanall |
</ | </ |
exercises/2015_ethz_mmm/alanine_dipeptide.1423244958.txt.gz · Last modified: 2020/08/21 10:14 (external edit)