events:2016_summer_school:qmmm
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events:2016_summer_school:qmmm [2016/08/25 11:03] – mwatkins | events:2016_summer_school:qmmm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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School of Mathematics and Physics, University of Lincoln, UK | School of Mathematics and Physics, University of Lincoln, UK | ||
- | http:// | + | https:// |
{{https:// | {{https:// | ||
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$$ | $$ | ||
- | Periodic electric field uses the Berry phase formalism of the [[http:// | + | Periodic electric field uses the Berry phase formalism of the [[https:// |
- | {{http:// | + | {{https:// |
- | [[http:// | + | [[https:// |
==== QM/MM ==== | ==== QM/MM ==== | ||
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Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins | Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins | ||
- | {{ exercises: | + | {{exercises: |
typically the active site was surrounded by a finite number of classical point charges | typically the active site was surrounded by a finite number of classical point charges | ||
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An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system. | An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system. | ||
- | {{exercises: | + | {{exercises: |
{{ exercises: | {{ exercises: | ||
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the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth. | the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth. | ||
- | {{http:// | + | The number of terms in the sum $N_g$ is set by the input variable '' |
+ | |||
+ | {{https:// | ||
- | [http:// | + | [[https:// |
== Short range electrostatic coupling - collocating the potential == | == Short range electrostatic coupling - collocating the potential == | ||
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</ | </ | ||
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The short range part is put onto grids in much the same manner as in the GPW method. | The short range part is put onto grids in much the same manner as in the GPW method. | ||
- | [[http:// | + | [[https:// |
== Periodic embedding == | == Periodic embedding == | ||
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section. The default is non periodic embedding. | section. The default is non periodic embedding. | ||
- | {{http:// | + | {{https:// |
- | [[http:// | + | [[https:// |
== Long range coupling == | == Long range coupling == | ||
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see this [[https:// | see this [[https:// | ||
- | ## Input files | + | ===== Input files ===== |
- | Example setup for KCl that we used [here](http:// | + | Example setup for KCl that we used [[https:// |
- | {{http:// | + | {{https:// |
We need to define the whole system as normal | We need to define the whole system as normal |
events/2016_summer_school/qmmm.1472123001.txt.gz · Last modified: 2020/08/21 10:14 (external edit)