exercises:2014_uzh_molsim:nacl_free_energy
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exercise:mm_uzh:nacl_free_energy [2014/05/16 17:11] – talirz | exercise:mm_uzh:nacl_free_energy [2014/06/30 11:25] – talirz | ||
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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 [[http:// |
</ | </ | ||
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< | < | ||
- | - What is a Lagrange multiplier? How can we obtain the free energy profile as a function of the Na-Cl distance using the associated Lagrange multiplier? | + | - What is a Lagrange multiplier? How can we obtain the free energy profile as a function of the Na-Cl distance using the associated Lagrange multiplier? |
- Run the simulation. What kind of motion does the NaCl dimer perform? | - Run the simulation. What kind of motion does the NaCl dimer perform? | ||
- | - Compare the low-temperature free energy profile in '' | + | - Compare the low-temperature free energy profile in '' |
- What effects would you expect at higher temperature? | - What effects would you expect at higher temperature? | ||
</ | </ | ||
Now, we are ready to move to a more realistic system -- NaCl in water. | Now, we are ready to move to a more realistic system -- NaCl in water. | ||
- | We have performed constrained MD of NaCl in water and saved the trajectory of the corresponding Lagrange multipliers. | + | We have performed constrained MD of NaCl in water and saved the trajectory of the corresponding Lagrange multipliers |
The script '' | The script '' | ||
< | < | ||
- 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 [[http:// |
</ | </ | ||
- | Another way to gain access to the free energy is through the radial distribution function (rdf). The rdf $g(r)$ is related to the free energy $F(r)$ through the following set of equations | + | Another way to gain access to the free energy is through the radial distribution function (rdf) of the // |
+ | The rdf $g(r)$ is related to the free energy $F(r)$ through the following set of equations | ||
$$\begin{eqnarray} | $$\begin{eqnarray} | ||
g(r)4\pi r^2 & | g(r)4\pi r^2 & | ||
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- | We have provided | + | We have performed |
< | < | ||
- | - In the [[http:// | + | - In the [[http:// |
- 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? | ||
</ | </ |
exercises/2014_uzh_molsim/nacl_free_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1