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exercises:2017_uzh_acpc2:mol_sol

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exercises:2017_uzh_acpc2:mol_sol [2017/05/04 15:02] – [Water] jglanexercises:2017_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-====== Potential energy surface of glyala dipeptide ======+====== Molecular Solution ======
  
 ===== Ramachandran plot ===== ===== Ramachandran plot =====
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 In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its //potential energy surface//. In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its //potential energy surface//.
  
-The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone.+The conformations of glyala 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.  Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. 
 the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone.
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   - 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.   - 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 ''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? <code> $ gnuplot</code><code> gnuplot >> load "epot.gp"</code>+  - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations? <code> $ gnuplot</code><code> gnuplot > load "epot.gp"</code>
 </note> </note>
 ===== Water ===== ===== Water =====
exercises/2017_uzh_acpc2/mol_sol.1493910170.txt.gz · Last modified: (external edit)