# 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 21:23]yakutovich exercises:2015_uzh_molsim:nacl_md [2015/05/27 14:13] (current)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 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  ​