CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
exercises:2014_uzh_molsim:h2o_diff

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
Next revisionBoth sides next revision
exercise:mm_uzh:h2o_diff [2014/05/12 19:45] – talirzexercise:mm_uzh:h2o_diff [2014/05/31 18:05] – talirz
Line 13: Line 13:
 Start the MD simulation for 32 water molecules and see how far you can get (aim at least for 200 ps). Start the MD simulation for 32 water molecules and see how far you can get (aim at least for 200 ps).
 <note tip> <note tip>
-This simulation will take some time. +This simulation will take a considerable amount of time. 
 Tasks 1 and 2 can already be completed, while it is running. Tasks 1 and 2 can already be completed, while it is running.
 </note> </note>
Line 20: Line 20:
   - We want to simulate diffusion at room temperature. Why aren't we using the $NVT$ ensemble? //Hint:// Think about how thermostats work.   - We want to simulate diffusion at room temperature. Why aren't we using the $NVT$ ensemble? //Hint:// Think about how thermostats work.
   - Use the provided script ''./get_t_sigma file.ener'' to calculate the standard deviation of the temperature for your simulation as well as for the provided simulations of larger cells containing 64, 128 and 256 water molecules.   - Use the provided script ''./get_t_sigma file.ener'' to calculate the standard deviation of the temperature for your simulation as well as for the provided simulations of larger cells containing 64, 128 and 256 water molecules.
-  - How are temperature fluctuations expected to depend on system size? Use gnuplot's fitting functionality to check whether they follow the corresponding law.+  - How are temperature fluctuations expected to depend on system size? Use gnuplot's fitting functionality to check whether they follow the corresponding law. //Hint:// See e.g. [[http://books.google.ch/books?id=5qTzldS9ROIC|"Understanding Molecular Simulations"]] by Frenkel and Smit, sections 4.1 and 6.2. (2P)
 </note> </note>
  
Line 40: Line 40:
 <note>**TASK 2** <note>**TASK 2**
  
-  - While your simulation is running, calculate the msd for the provided simulations of 64, 128 and 256 water molecules, modifying ''msd.in'' as needed. //Note:// ''msd.x'' may run up to 30 minutes for the largest cell. +  - We have precalculated trajectories for 64, 128 and 256 water molecules (ask your teaching assistant). Use ''msd.x'' to calculate the msd, modifying ''msd.in'' as needed. //Note:// ''msd.x'' may run up to 30 minutes for the largest cell. 
-  - Plot the msd as a function of time on a double logarithmic scale. Can you identify different regimes? Why does the signal become noisy towards long times?+  - Plot the msd as a function of time on a double logarithmic scale. Can you identify different regimes? Why does the signal become noisy towards long times? (2P)
   - Obtain the diffusion constant $D_{pbc}$ by fitting a line through the mean square displacement data in the range $2-10$ ps.   - Obtain the diffusion constant $D_{pbc}$ by fitting a line through the mean square displacement data in the range $2-10$ ps.
   - Compare against the values in Table I of the article. //Note:// We are using a slightly different force field, but the values should be  of a similar magnitude. If not, check your units!   - Compare against the values in Table I of the article. //Note:// We are using a slightly different force field, but the values should be  of a similar magnitude. If not, check your units!
 </note> </note>
  
-When your MD of the 32 water molecules has finished, you can start fitting the diffusion constant.+When your MD of the 32 water molecules has finished (for example on the next day), you can start fitting the diffusion constant.
 <note>**TASK 3** <note>**TASK 3**
  
Line 52: Line 52:
   - Plot $D_{PBC}$ as a function of $1/L$, where $L$ is the length of the edge of the simulation box.   - Plot $D_{PBC}$ as a function of $1/L$, where $L$ is the length of the edge of the simulation box.
   - Perform a linear fit of this curve to obtain the diffusion constant $D=D_{pbc}(L=\infty)$   - Perform a linear fit of this curve to obtain the diffusion constant $D=D_{pbc}(L=\infty)$
-  - Use Eq. 12 in the article to calculate the viscosity.+  - Use equation (12) in the article to calculate the viscosity $\eta$ from the slope of $D_{PBC}(1/L)$.
   - Compare the results to the data in the paper.   - Compare the results to the data in the paper.
 </note> </note>
exercises/2014_uzh_molsim/h2o_diff.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1