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--- exercise:mm_uzh:nacl_md [2014/05/19 21:51] – talirz
+++ exercises:2014_uzh_molsim:nacl_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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   - Look inside ''free.in'', report which interactions are considered and how they are modeled. Can you write down the Hamiltonian? //Hint:// For inspiration, you may want to once again have a look into the paper by [[doi>10.1063/1.1884609|Praprotnik et al.]]. (2P)
-  - Determine the concentration of $\text{NaCl}$ in the simulation in units of mol per liter. Do you consider the solution to be dilute?
+  - Ideally, we would like to study isolated $\text{NaCl}$ ion pairs. Determine the concentration of $\text{NaCl}$ in the simulation in units of mol per liter. Do you consider the solution to be dilute?
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   - Describe the effect of the Na-Cl distance on the different rdfs. //Note:// The radial distribution function computed here only considers atom pairs A and B from //different molecules//. (2P)
   - How is the coordination number $n_1$ defined? Give an analytical formula to compute it from the rdf.
-  - Calculate the first coordination number of Na from the Na-O rdf using the script ''./integrate.py --N=<Natoms> --L=<BoxLength> < gofr_A_B-X.Y > nc_A_B-X.y'' where ''<Natoms>'' is the number of ''B'' atoms per cell and ''<BoxLength>'' the length of the simulation box in $\unicode{x212B}$.
+  - Calculate the first coordination number of Na from the Na-O rdf using the script ''./integrate.py %%--%%N=<Natoms> %%--%%L=<BoxLength> < gofr_A_B-X.Y > nc_A_B-X.y'' where ''<Natoms>'' is the number of ''B'' atoms per cell and ''<BoxLength>'' the length of the simulation box in $\unicode{x212B}$.
   - How does the coordination number of Na with respect to O vary with the constrained Na-Cl distance? What does this mean for the coordination of Na?
 </note>