Check reaction ensemble tutorial with current HEAD #3211
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I suggest to remove this old tutorial. |
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Oct 17, 2019
3252: Factor out ParticleList r=jngrad a=fweik Follow up on #3251. Description of changes: - Pulling `ParticleList` out of `particle_data.hpp` to get better header disentanglement. 3256: Remove tutorial 10 and unused LaTeX files r=fweik a=jngrad Closes #3211 Description of changes: - removed tutorial 10 - removed unused LaTeX preambles 3257: Remove PDB parser feature r=fweik a=jngrad The consensus offline at the ICP and online in #1441 is to drop support of the PDB parser feature in favor of the dedicated python package MDAnalysis. Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>
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Oct 17, 2019
3252: Factor out ParticleList r=jngrad a=fweik Follow up on #3251. Description of changes: - Pulling `ParticleList` out of `particle_data.hpp` to get better header disentanglement. 3256: Remove tutorial 10 and unused LaTeX files r=fweik a=jngrad Closes #3211 Description of changes: - removed tutorial 10 - removed unused LaTeX preambles 3257: Remove PDB parser feature r=fweik a=jngrad The consensus offline at the ICP and online in #1441 is to drop support of the PDB parser feature in favor of the dedicated python package MDAnalysis. Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>
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Oct 23, 2019
3184: some modifications to constant-pH tutorial r=KaiSzuttor a=kosovan Fixes #3211 TODO (will do): - [x] First , explain how the reaction works, then discuss the acceptance - [x] Define pH, pK, activity and its relation chemical potential and concentration - [x] Refer to original literature for the acceptance, refer to review paper for discussion of peculiarities and pitfalls - [x] Include all physical parameters of the simulated system (box_l, N0, pKa, pH_range) in one block at the beginning of the script - [x] Set N0 and concentration in SI units, calculate box_l in sigma - [x] restrict the range of pH values to pH in [pK-2:pK+2] - [x] Remove the discussion of standard error of the mean, refer to Janke instead (statistical analysis is not the learning goal of this tutorial) - [x] Samples of alpha are correlated. Therefore, apply blocking method or some other analysis of correlated samples. - [x] Remove the comparison of histograms, or define a learning goal for this part. Currently, the comparison suggests that constant-pH results differ from theory, while the actual reason for this is insufficient sampling. For a sufficiently long simulations, they should not differ. This is very confusing, especially if it is not explained. Description of changes: - PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Peter Košovan <[email protected]> Co-authored-by: Jonas Landsgesell <[email protected]> Co-authored-by: Peter Košovan <[email protected]> Co-authored-by: Peter Kosovan <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>
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