CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
exercises:2015_ethz_mmm:alanine_dipeptide

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/27 07:58] – dpasseroneexercises:2015_ethz_mmm:alanine_dipeptide [2015/03/03 22:26] – dpasserone
Line 1: Line 1:
 ====== Ramachandran plot for Alanine Dipeptide ====== ====== Ramachandran plot for Alanine Dipeptide ======
 +
 +<note warning>
 +TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE IN DANIELE PASSERONE DIR) IN THE INTERACTIVE SHELL:
 +you@eulerX ~$ . ~danielep/Scripts/m_functions.bash
 +</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.
Line 24: Line 29:
 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>
  
Line 139: Line 144:
  
 <code> <code>
-you@brutusX exercise_2.2$ module load new cp2k +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>
  
Line 147: Line 152:
  
 <code> <code>
-you@brutusX exercise_2.2$ gnuplot torsion.gnu+you@eulerX exercise_2.2$ gnuplot torsion.gnu
 </code> </code>
  
Line 154: Line 159:
 m_pdbtorsion: m_pdbtorsion:
 <code> <code>
-you@brutusX exercise_2.2/Logs$ m_pdbtorsion 5 7 9 15 ; m_pdbtorsion 7 9 15 17 +you@eulerX exercise_2.2/Logs$ m_pdbtorsion 5 7 9 15 ; m_pdbtorsion 7 9 15 17 
 </code> </code>
  
Line 164: Line 169:
  
 <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