CP2K Open Source Molecular Dynamics

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exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:09] – jglanexercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:14] – [Water] jglan
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 We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|Praprotnik et al.]]). We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|Praprotnik et al.]]).
-<note important>Download {{ water.zip |water.zip}}</note> +<note important>Download {{ water.zip |water.zip}} and extract it.</note> 
  
  
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   * Does IR or dielectric constant match the experimenal value? If not, why?   * Does IR or dielectric constant match the experimenal value? If not, why?
 </note> </note>
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 ===== Ramachandran plot ===== ===== Ramachandran plot =====
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 Visualize the structure ''glyala.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles. Visualize the structure ''glyala.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles.
 </note> </note>
 +
 +<note important>//Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1.</note>
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 With this knowledge at hand, With this knowledge at hand,
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 <note>**TASK 2** <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.+  - 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. 
   - 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>
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 ===== Glyala in water ===== ===== Glyala in water =====
 Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory. Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory.
exercises/2018_uzh_acpc2/mol_sol.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1