CP2K Open Source Molecular Dynamics

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exercise:mm_uzh:h2o_ff [2014/05/18 16:07] – talirzexercise:mm_uzh:h2o_ff [2014/06/30 09:38] – talirz
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 <note>**TASK 4**  <note>**TASK 4** 
   - How many normal modes does the water molecule have and why?   - How many normal modes does the water molecule have and why?
-  - Compare the vibrational frequencies to the experimental ones given in the work by Praprotnik et al. Should they be identical? [[doi>10.1021/jp046158d|Hint]]. (2P)+  - Praprotnik et al. provide vibrational frequencies of the TIP3P model as well as experimental results from gas phase infrared spectroscopy. Compare them to your results and discuss the differences. //Hint:// [[doi>10.1021/jp046158d|Hint]]. (2P)
   - **BONUS** In order to complete our water model, we need the force constants and not the frequencies. Calculate the force constants directly from the frequencies. See e.g. [[http://books.google.ch/books?id=bE-9tUH2J2wC&hl=de|Landau-Lifshitz]], chapter V – //Vibrations of molecules//. (3P)   - **BONUS** In order to complete our water model, we need the force constants and not the frequencies. Calculate the force constants directly from the frequencies. See e.g. [[http://books.google.ch/books?id=bE-9tUH2J2wC&hl=de|Landau-Lifshitz]], chapter V – //Vibrations of molecules//. (3P)
 </note> </note>
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 In order to be applicable to a wide range of potentials, the implementation of the parameter search in CP2K does not rely on analytic derivatives of the potentials with respect to the parameters, but uses the trial- and error-like [[doi>10.1093/comjnl/7.2.155|Powell]] search algorithm. In order to be applicable to a wide range of potentials, the implementation of the parameter search in CP2K does not rely on analytic derivatives of the potentials with respect to the parameters, but uses the trial- and error-like [[doi>10.1093/comjnl/7.2.155|Powell]] search algorithm.
  
-In ''ff_match.in'', replace the DUMMY values for the equilibrium O-H bond length, H-O-H angle and the point charges by the parameters determined before. Copy the trajectory ''run-1H2O-AIMD.xyz'' and the forces ''run-1H2O-AIMD.force'' to the new directory and replace the dummy filenames in ''ff_match.in''. Run ''ff_match.in'' to fit the stretching and bending force constants via force matching.+In ''ff_match.in'', replace the dummy values for the preferred O-H bond length, H-O-H angle and the point charges by the parameters determined from the geometry optimization and the RESP fit. Copy the trajectory ''run-1H2O-AIMD.xyz'' and the forces ''run-1H2O-AIMD.force'' to the new directory and replace the dummy filenames in ''ff_match.in''. Run ''ff_match.in'' to fit the stretching and bending force constants via force matching. 
 + 
 +//Note:// Since we are considering an isolated water molecule, the Lennard-Jones interactions are explicitly set to zero in ''ff_match.in''.
 <note>**TASK 6**  <note>**TASK 6** 
  
exercises/2014_uzh_molsim/h2o_ff.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1