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exercises:2014_uzh_molsim:alanine_dipeptide

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exercise:mm_uzh:alanine_dipeptide [2014/06/11 11:48] – talirzexercises:2014_uzh_molsim:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone. the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone.
  
-{{ :exercise:mm_uzh:alanine.png?direct&400 |}}+{{ alanine.png?direct&400 |}}
  
 <note>**TASK 1** <note>**TASK 1**
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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 gunplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations?+  - 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]].   - Compare with Figure 3 of [[doi>10.1073/pnas.100127697]].
 </note> </note>
exercises/2014_uzh_molsim/alanine_dipeptide.1402487319.txt.gz · Last modified: 2020/08/21 10:14 (external edit)