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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
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   - 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)
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 <​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)
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 <​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?​
 </​note>​ </​note>​
exercises/2014_uzh_molsim/nacl_free_energy.txt ยท Last modified: 2014/10/15 13:44 by oschuett