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--- exercises:2018_uzh_acpc2:mol_sol [2018/05/04 14:09] – jglan
+++ exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:09] – jglan
@@ Line 4: / Line 4: @@
 [[http://www1.lsbu.ac.uk/water/water_models.html|Water molecular models]] are computational techniques that have been developed in order to help discover the structure of water. In this section, you will be asked to calculate some physical properties based on classical molecular dynamics simulation. The TIP3/Fw model will be usded in the simulations.
-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.]]). Download {{ water.zip |water.zip}}
+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>
@@ Line 32: / Line 33: @@
   * Plot RMSD for the water at 300K and calculate corresponding diffusion coefficient, are they expected?
 </note>
+<note important>The diffusion coefficient is calculated using MSD but NOT RMSD.</note>
 We will compute the vibrational spectrum, and dielectric constant of water based on molecular dynamics. The spectra for water are available in this paper [[https://aip.scitation.org/doi/pdf/10.1063/1.1884609|https://doi.org/10.1063/1.1884609]]. The provided program computes the correlation function of the (derivative of) the dipole moment and performs the Fourier transform.