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exercises:2015_uzh_molsim:alanine_dipeptide

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exercises:2015_uzh_molsim:alanine_dipeptide [2015/05/26 21:26]
yakutovich
exercises:2015_uzh_molsim:alanine_dipeptide [2020/08/21 10:15]
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-====== Potential energy surface of alanine dipeptide ====== 
  
-Alanine dipeptide is one of the simplest molecules that exhibits some important features common to larger biomolecules. 
-In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its //potential energy surface//. 
- 
-<note tip> 
-Our "alanine dipeptide" is actually slightly modified: 
- 
-The carboxylate is replaced by an acyl group (C-terminus) and the primary amine is converted into a secondary amine by the addition of a methyl group (N-terminus). 
- 
-</note> 
- 
-The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone. 
-Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e.  
-the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone. 
- 
-{{ alanine.png?direct&400 |}} 
- 
-<note>**TASK 1** 
-Visualize the structure ''a1a2ene.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles. 
-</note> 
- 
-With this knowledge at hand, 
-we will fix the dihedral angles and perform geometry optimization for all remaining degrees of freedom. 
- 
-<note>**TASK 2** 
- 
-  - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by the atomic indices determined previously. //Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1. 
-  - Use ''perform-gopt.sh'' to perform the grid of geometry optimizations. 
-  - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations? 
-  - Compare with Figure 3 of [[doi>10.1073/pnas.100127697]]. 
-</note> 
exercises/2015_uzh_molsim/alanine_dipeptide.txt ยท Last modified: 2020/08/21 10:15 (external edit)