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--- exercise:mm_uzh:h2o_md [2014/05/02 17:16] – talirz
+++ exercise:mm_uzh:h2o_md [2014/05/02 17:19] – [Infrared spectrum] talirz
@@ Line 39: / Line 39: @@
 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>
 gfortran dipole_correlation.f90 -o dipole_correlation.x  # compile fortran program