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--- exercise:mm_uzh:nacl_md [2014/05/19 21:48] – talirz
+++ exercise:mm_uzh:nacl_md [2014/05/20 06:14] – talirz
@@ Line 39: / Line 39: @@
 <note>**TASK 3**
-  - Open one of the files ''gofr_A_B'' in a text editor to understand their structure. Use gnuplot with ''splot "gofr_A_B"'' to analyze the rdfs as a function of the constraint.
+  - Use gnuplot to analyze the rdfs as a function of the constraint. //Note:// You may use either the individual ''gofr_A_B_X.Y'' or the joined files ''gofr_A_B'' (here, use ''splot'').
   - 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>