User Tools

Site Tools


exercises:2014_uzh_molsim:nacl_free_energy

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
Last revisionBoth sides next revision
exercise:mm_uzh:nacl_free_energy [2014/05/19 22:34] talirzexercise:2014_uzh_molsim:nacl_free_energy [2014/10/15 13:44] oschuett
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)
 </note> </note>
  
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)
 </note> </note>
  
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 reasonable statistics using just 20 ps of simulated time. Give at least one reason, 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 · Last modified: 2020/08/21 10:15 by 127.0.0.1