Add AHFE tutorial by hannahbaumann · Pull Request #100 · OpenFreeEnergy/ExampleNotebooks

hannahbaumann · 2024-02-22T14:27:16Z

No description provided.

github-actions · 2024-02-22T14:27:27Z

👈 Launch a binder notebook on branch OpenFreeEnergy/ExampleNotebooks/ahfe_tutorial

IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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To be discussed - I think some kind of diagramatic representation of the transformation might be worth it here? Like some kind of thermodynamic cycle figure?

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IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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(I know it's in the inline comment, but maybe it would be worth moving it here under a sub-heading?): we should mention what the endstates are in terms of chemicalsystems, i.e. hydration free energy of ligand is ligand+water to water.

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Added this!

IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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Would it be worth adding an in-line explanation of what the setting is?

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Added this!

IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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It would be good to offer a short overview of what the default settings are and what we are changing here. Nothing too fancy, just a "by default we run N repeats with solvent & vacuum simulation lengths of Y and Z over L lambda windows, to speed things up here we instead do...".

Maybe also worth bringing down the number of repeats to 1 to speed up the notebook?

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Added this!

IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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You should be able to just call settings here and get the pprint dictionary output.

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IAlibay · 2024-03-04T06:25:07Z

ahfe_tutorial/python_tutorial.ipynb

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We don't have a way to gather results from CLI right now. Maybe it's worth saving the Python API results to disk and then here we re-load them? Not sure if that's too complicated for users though.

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IAlibay

Overall looks good! Just added some early comments (I know it's still WIP).

review-notebook-app · 2024-03-04T23:26:17Z

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IAlibay · 2024-03-06T17:40:53Z

@hannahbaumann I've added the results json by quick-running the benzene.json that was already there, just checking if this is what you needed?

hannahbaumann · 2024-03-25T13:27:42Z

I added a short thing about reloading a json file, does this look good @IAlibay ?

IAlibay · 2024-03-26T10:04:40Z

ahfe_tutorial/python_tutorial.ipynb

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[enhancement] Something I found out recently, apparently you can use greek alphabet in jupyter notebooks using the \ command, so \Delta might work (I never tried it in practice).
re: "decoupled", I'm not sure if it would be too complicated for readers so feel free to say no - do you think that setting this as "partially decoupled (annihilated coulombics, decoupled Lennard-Jones)" might be worth it? (it makes it quite the sentence, so maybe not)

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Added a sentence describing this.

IAlibay · 2024-03-26T10:04:40Z

ahfe_tutorial/python_tutorial.ipynb

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This is amazing!

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IAlibay · 2024-03-26T10:04:40Z

ahfe_tutorial/python_tutorial.ipynb

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+{


I've been trying to think about the information flow here, how about something like this:

"
Finally now that we've run our simulations, let's go ahead and gather the free energies for both phases.

Python API

If you executed the simulations using the Python API, you will have generated a dag_results object. You can analyze these results by calling the Protocols' gather() method. This takes a list of completed DAG results and returns a AbsoluteSolvationProtocolResult which can return a free energy estimate and uncertainty by calling the get_estimate() and get_uncertainty() methods."

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IAlibay · 2024-03-26T10:04:40Z

ahfe_tutorial/python_tutorial.ipynb

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+{


Then above this cells we could say:

"You can save the AbsoluteSolvationProtocolResult to a JSON output file in the following manner:"

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IAlibay · 2024-03-26T10:04:41Z

ahfe_tutorial/python_tutorial.ipynb

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And here above this one:

"
CLI / Quickrun

If you ran the simulation using the CLI (i.e. by calling openfe quickrun ) you will end up with the same JSON output file as the one created in the previous cell. To get your simulation results you can load them back into Python in the following manner:
"

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IAlibay · 2024-03-26T10:05:27Z

This is looking great! Just a couple of text suggestions for the last section (mostly trying to be a bit more verbose).

IAlibay

This is great, thanks!

IAlibay · 2024-03-26T13:56:03Z

Just in case - I pushed 1fc6666 to update the settings outputs (the checkpoint default value changed)

adding ahfe tutorial

0c03dbf

hannahbaumann added 2 commits February 22, 2024 16:28

add results

2f1d541

add quickrun example

aef1036

IAlibay reviewed Mar 4, 2024

View reviewed changes

changes addressing some of the review comments

0163d5a

hannahbaumann added 2 commits March 5, 2024 14:33

add json, add thermodynamic cycle

15cd4bf

small fix

aaf647d

richardjgowers mentioned this pull request Mar 6, 2024

quick demo script based on ahfe tutorial in ExampleNotebooks OpenFreeEnergy/openfe_skunkworks#7

Closed

Add results json

f829ebb

Load results from json

4d5681c

small changes

486364d

hannahbaumann changed the title ~~[WIP] Add AHFE tutorial~~ Add AHFE tutorial Mar 25, 2024

richardjgowers assigned IAlibay Mar 25, 2024

IAlibay reviewed Mar 26, 2024

View reviewed changes

Addressing comments

8094bcd

IAlibay approved these changes Mar 26, 2024

View reviewed changes

udpate ahfe tutorial metadata

1fc6666

IAlibay merged commit 556705f into main Mar 26, 2024

IAlibay deleted the ahfe_tutorial branch March 26, 2024 13:56

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