# Open SourceMolecular Dynamics

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exercises:2014_uzh_molsim:nacl_free_energy

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 exercises:2014_uzh_molsim:nacl_free_energy [2014/06/30 11:25]talirz exercises:2014_uzh_molsim:nacl_free_energy [2014/10/15 13:44] (current)oschuett Both sides previous revision Previous revision 2014/10/15 13:44 oschuett 2014/06/30 11:25 talirz 2014/05/19 22:34 talirz 2014/05/19 21:45 talirz 2014/05/16 17:11 talirz 2014/05/16 17:07 talirz 2014/05/16 16:00 talirz added task 42014/05/16 15:09 talirz 2014/05/16 15:08 talirz added task 32014/05/16 14:58 talirz added task 22014/05/16 14:45 talirz created 2014/10/15 13:44 oschuett 2014/06/30 11:25 talirz 2014/05/19 22:34 talirz 2014/05/19 21:45 talirz 2014/05/16 17:11 talirz 2014/05/16 17:07 talirz 2014/05/16 16:00 talirz added task 42014/05/16 15:09 talirz 2014/05/16 15:08 talirz added task 32014/05/16 14:58 talirz added task 22014/05/16 14:45 talirz created Line 8: Line 8: - Look into ''​NaCl_pot.in''​ and write down the formula used for the potential energy of the interaction between $\text{Na}^+$ and $\text{Cl}^-$ in Hartree atomic units. (2P) - Look into ''​NaCl_pot.in''​ and write down the formula used for the potential energy of the interaction between $\text{Na}^+$ and $\text{Cl}^-$ in Hartree atomic units. (2P) - Use ''​./​potential_energy.sh''​ to calculate the potential energy as a function of Na-Cl distance. Create a plot of the resulting potential energy profile in ''​pot_profile''​ and the mathematical formula. - Use ''​./​potential_energy.sh''​ to calculate the potential energy as a function of Na-Cl distance. Create a plot of the resulting potential energy profile in ''​pot_profile''​ and the mathematical formula. - - What do you observe, when the distance approaches 1/2 of the simulation box? How might the finite size of the simulation box have impacted the MD simulation in the [[http://​cp2k.org/​exercise:​mm_uzh:​nacl_md|previous exercise]]? (2P) + - What do you observe, when the distance approaches 1/2 of the simulation box? How might the finite size of the simulation box have impacted the MD simulation in the [[nacl_md|previous exercise]]? (2P) ​ Line 29: Line 29: <​note>​**TASK 3** <​note>​**TASK 3** - Perform the free energy integration and plot the free energy profile. - Perform the free energy integration and plot the free energy profile. - - In the [[http://​cp2k.org/​exercise:​mm_uzh:​nacl_md|previous exercise]], you determined the average time required for dissociation of Na-Cl. Is the free energy barrier consistent with the time scale determined before? //Hint:// Use the Arrhenius equation. You can obtain an estimate for the attempt frequency from the high-frequency oscillations in the Na-Cl distance in the previous exercise. (2P) + - In the [[nacl_md|previous exercise]], you determined the average time required for dissociation of Na-Cl. Is the free energy barrier consistent with the time scale determined before? //Hint:// Use the Arrhenius equation. You can obtain an estimate for the attempt frequency from the high-frequency oscillations in the Na-Cl distance in the previous exercise. (2P) ​ Line 44: Line 44: <​note>​**TASK 4** <​note>​**TASK 4** - - In the [[http://​cp2k.org/​exercise:​mm_uzh:​h2o_md|previous exercise]], we computed the O-O radial distribution function for water with acceptable statistics using just 20 ps of simulated time. Give two reasons, why collecting enough statistics for the Na-Cl radial distribution function requires much longer simulation times (with our setup). + - In the [[h2o_md|previous exercise]], we computed the O-O radial distribution function for water with acceptable statistics using just 20 ps of simulated time. Give two reasons, why collecting enough statistics for the Na-Cl radial distribution function requires much longer simulation times (with our setup). - Compute the radial distribution function for the provided trajectory and plot it as a function of Na-Cl distance. - Compute the radial distribution function for the provided trajectory and plot it as a function of Na-Cl distance. - Use the equations above to compute the free energy profile. Does it agree with the one constructed from the Shake Lagrange multipliers?​ - Use the equations above to compute the free energy profile. Does it agree with the one constructed from the Shake Lagrange multipliers?​