exercises:2014_uzh_molsim:h2o_diff
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exercise:mm_uzh:h2o_diff [2014/05/12 19:39] – talirz | exercises:2014_uzh_molsim:h2o_diff [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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When simulating liquids or solids under periodic boundary conditions, we are making two fundamental approximations: | When simulating liquids or solids under periodic boundary conditions, we are making two fundamental approximations: | ||
- | - We simulate an infinite system, thus neglecting the fact that any real-world system | + | - We simulate an infinite system, thus neglecting the fact that any real-world system |
- We impose the condition that the properties of the system under study repeat //exactly// from one simulation cell to the next. The quality of this approximation depends on the system under study and the quantity of interest. | - We impose the condition that the properties of the system under study repeat //exactly// from one simulation cell to the next. The quality of this approximation depends on the system under study and the quantity of interest. | ||
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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. | ||
</ | </ | ||
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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 '' | - Use the provided script '' | ||
- | - How are temperature fluctuations expected to depend on system size? Use gnuplot' | + | - How are temperature fluctuations expected to depend on system size? Use gnuplot' |
</ | </ | ||
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./msd.x < msd.in | ./msd.x < msd.in | ||
</ | </ | ||
- | Per default, the msd is written | + | Per default, |
Once you have calculated the msd, have a look into section III of the article on how to fit the diffusion constant. | Once you have calculated the msd, have a look into section III of the article on how to fit the diffusion constant. | ||
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< | < | ||
- | - While your simulation is running, calculate the msd for the provided simulations of 64, 128 and 256 water molecules, modifying '' | + | - We have precalculated trajectories |
- | - Plot the msd as a function of time using 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? |
- | - 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. //Note:// We are using a slightly different force field, but the values should be similar. 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 |
</ | </ | ||
- | 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 |
< | < | ||
- | - Calculate | + | - Calculate $D_{PBC}(L)$ |
- 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 |
- Compare the results to the data in the paper. | - Compare the results to the data in the paper. | ||
</ | </ |
exercises/2014_uzh_molsim/h2o_diff.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1