CP2K Open Source Molecular Dynamics

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exercises:2014_uzh_molsim:h2o_diff

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exercise:mm_uzh:h2o_diff [2014/05/12 20:27] – talirzexercise:mm_uzh:h2o_diff [2014/05/13 11:54] – talirz
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   - 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. (2P)
 </note> </note>
  
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   - 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.   - 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!
exercises/2014_uzh_molsim/h2o_diff.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1