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exercises:2014_uzh_molsim:h2o_md

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exercise:mm_uzh:h2o_md [2014/05/02 17:16] – talirzexercise:mm_uzh:h2o_md [2014/05/02 17:20] – talirz
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 In MD simulations, these frequencies can be extracted from the autocorrelation function of the total dipole moment of all charges in the simulation box. In MD simulations, these frequencies can be extracted from the autocorrelation function of the total dipole moment of all charges in the simulation box.
  
-Repeat the MD at 300 K, but now uncomment the ''&DIPOLE'' section in the  input file in order to write the dipole to ''dipole.traj''.  +Repeat the MD at 300 K, but now uncomment the ''&DIPOLE'' section in the  input file in order to write the total dipole moment to ''dipole.traj''.
-Once the simulation is finished, calculate the autocorrelation function.+
  
-We have provided a short Fortran program ''dipole_correlation.f90'' to do this. Use the ''gfortran'' compiler to generate the executable and calculate the dipole-autocorrelation function (adjusting its input file  ''dipole.in'' as needed):+We have provided a short Fortran program ''dipole_correlation.f90'' to calculate the autocorrelation function. 
 +Use the ''gfortran'' compiler to generate the executable and, once the MD simulation is finished, use it to calculate the dipole-autocorrelation function (adjusting its input file  ''dipole.in'' as needed):
 <code bash> <code bash>
 gfortran dipole_correlation.f90 -o dipole_correlation.x  # compile fortran program gfortran dipole_correlation.f90 -o dipole_correlation.x  # compile fortran program
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 <note>**TASK 4** <note>**TASK 4**
  
-  * What are the estimate frequencies of the stretching and bending modes?+  * What are the approximate frequencies of the stretching and bending modes?
   *  How do they compare to the normal mode frequencies of the isolated molecule? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum.   *  How do they compare to the normal mode frequencies of the isolated molecule? Use a longer simulation time (e.g. 40 ps) to obtain a clearer spectrum.
   * Perform a simulation with a larger time step (e.g. 1.5 fs). What is the effect on the spectrum? Provide graphs of both spectra in the report.   * Perform a simulation with a larger time step (e.g. 1.5 fs). What is the effect on the spectrum? Provide graphs of both spectra in the report.
   * Compare with Figure 3 in the paper of Praprotnik et al.   * Compare with Figure 3 in the paper of Praprotnik et al.
 </note> </note>
exercises/2014_uzh_molsim/h2o_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1