CP2K Open Source Molecular Dynamics

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exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:12] – [Ramachandran plot] jglanexercises:2018_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1
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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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 </note> </note>
  
-<note important>The index number in VMD is different from the number in CP2K, as the index start from 0 in VMD, 1 in CP2K. Thus, one need to specify index number + 1 obtained from VMD</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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 <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