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exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/27 07:58]
dpasserone
exercises: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 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>​
  
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 <​code>​ <​code>​
-you@brutusX ​exercise_2.2$ gnuplot torsion.gnu+you@eulerX ​exercise_2.2$ gnuplot torsion.gnu
 </​code>​ </​code>​
  
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 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>​
  
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 <​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: 2015/03/06 02:40 by dpasserone