# Open SourceMolecular Dynamics

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exercises:2015_uzh_molsim:nacl_md

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 exercises:2015_uzh_molsim:nacl_md [2015/05/26 21:20]yakutovich exercises:2015_uzh_molsim:nacl_md [2015/05/27 14:13]yakutovich Both sides previous revision Previous revision 2015/05/27 14:13 yakutovich 2015/05/26 21:23 yakutovich 2015/05/26 21:20 yakutovich 2015/04/23 12:20 external edit Next revision Previous revision 2015/05/27 14:13 yakutovich 2015/05/26 21:23 yakutovich 2015/05/26 21:20 yakutovich 2015/04/23 12:20 external edit Line 7: Line 7: - 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? - 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? ​ - When collecting statistics by successive MD runs, one often wants initial conditions to be random in order for the runs to be statistically independent. At the same time, it is often desirable for MD simulations to be exactly reproducible. When collecting statistics by successive MD runs, one often wants initial conditions to be random in order for the runs to be statistically independent. At the same time, it is often desirable for MD simulations to be exactly reproducible. Line 23: Line 22: In order to compute the Na-Cl distance within vmd, use the Tcl interface In order to compute the Na-Cl distance within vmd, use the Tcl interface - pbc set { lx ly lz }  # define simulation box lx*ly*lz + pbc set { lx ly lz } -all # define simulation box lx*ly*lz # center the box around Na and wrap all atoms into the box # center the box around Na and wrap all atoms into the box pbc wrap -centersel "​element Na" -center com -all  ​ pbc wrap -centersel "​element Na" -center com -all  ​ Line 42: Line 41: - How is the coordination number $n_1$ defined? Give an analytical formula to compute it from the rdf. - 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? + - 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? How to explain the linear increase of Na-O coordination number after 4 angstroms (should be cubic, right?)? (2P) 