CP2K Open Source Molecular Dynamics

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exercises:2017_uzh_acpc2:mol_sol [2017/05/09 08:23] – [Ramachandran plot] jglanexercises:2017_uzh_acpc2:mol_sol [2017/05/17 13:23] – jglan
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-====== Potential energy surface of glyala dipeptide ======+====== Molecular Solution ======
  
 ===== Ramachandran plot ===== ===== Ramachandran plot =====
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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.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1