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exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/26 15:35] yakutovichexercises:2015_ethz_mmm:alanine_dipeptide [2015/03/06 02:40] dpasserone
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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
 +</note>
 +
  
 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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 Then go to the directory “exercise_2.2/ Then go to the directory “exercise_2.2/
 <code> <code>
-you@brutusX ~$ cd exercise_2.2+you@eulerX ~$ cd exercise_2.2
 </code> </code>
  
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 <code> <code>
-you@brutusX exercise_2.2$ module load cp2k/trunk.2.5.13191 +you@eulerX exercise_2.2$ module load new cp2k 
-you@brutusX exercise_2.2$ bsub < grid_alanine+you@eulerX exercise_2.2$ bsub < grid_alanine
 </code> </code>
  
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 <code> <code>
-you@brutusX exercise_2.2$ gnuplot dihedral.gnu+you@eulerX exercise_2.2$ gnuplot torsion.gnu
 </code> </code>
  
 +<note important>
 +Changing into the directory **Logs** you fill find files of the kind **opt.?.?.pdb** . You can now verify that the target torsional angles have been reached. To this end you can either use the graphical program **vmd** (first, load the module with **module load vmd**) or the function 
 +m_pdbtorsion:
 +<code>
 +you@eulerX exercise_2.2/Logs$ m_pdbtorsion 5 7 9 15 ; m_pdbtorsion 7 9 15 17 
 +</code>
 +
 +for the two dihedral **Phi** and **Psi**.
 +
 +
 +</note>
 To clean the output and unnecessary files and do it again, To clean the output and unnecessary files and do it again,
  
 <code> <code>
-you@brutusX exercise_2.2$ ./cleanall+you@eulerX exercise_2.2$ ./cleanall
 </code> </code>
exercises/2015_ethz_mmm/alanine_dipeptide.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1