exercises:2014_uzh_molsim:nacl_free_energy
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exercise:mm_uzh:nacl_free_energy [2014/05/19 22:34] – talirz | exercise:2014_uzh_molsim:nacl_free_energy [2014/10/15 13:44] – oschuett | ||
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- Look into '' | - Look into '' | ||
- Use '' | - Use '' | ||
- | - 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:// | + | - 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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< | < | ||
- 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:// | + | - 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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< | < | ||
- | - In the [[http:// | + | - In the [[h2o_md|previous exercise]], we computed the O-O radial distribution function for water with acceptable |
- 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? | ||
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exercises/2014_uzh_molsim/nacl_free_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1