Add tutorial for MD simulations #97

hannahbaumann · 2024-02-16T15:04:31Z

No description provided.

github-actions · 2024-02-16T15:04:43Z

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

hannahbaumann · 2024-02-16T16:12:37Z

I added this as a tutorial, but could also be a cookbook instead.

IAlibay · 2024-03-04T05:08:30Z

Just cycling this PR in the hope that reviewnb kicks in.

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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[enhancement]

What would be super useful here is some kind of rough table of how the protocol works like

Input handling using gufe
Parameterization using OpenMMForceFields & OpenFF
OpenMM object creation
Minimization
NVT equilibration (if not gas phase)
NPT equilibration (if not gas phase)
NPT production (if not gas phase)

The table could have the columns "step", "software used", and "outputs". That way folks know what files come out of which steps.

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Added a table describing these steps.

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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We can probably go without the "when creating the OpenMM simulation objects" since those aren't exposed to users.

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Removed this

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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1)

The bullet points go from 8 to 10 (also there's a weird indentation for 10).

If you felt like it, it might be worth seeing if a table format might be cleaner here (but that's really just if you want to play around with formatting).

2)

"not the entire system with all the atoms should be saved" - a bit nitpicky, but this is a bit difficult to read because of the "not". Maybe "Special output indices can be defined to select which portions of the system should be saved" (it's the same but without the "not"). We should also make it clear as to what the default is (I think it's "not water"?)

It would be good to highlight the specific attributes that would need changing if possible. e.g. output_indices.

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That's a good idea! I moved the bullet points into a table, changed the sentence to your suggestion and changed some of the descriptions to highlight the code attributes. I hope this is intuitive for the user.

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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Line #6. settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond

[enhancement]

To help the reader, it may be worth adding inline comments here about what these are doing?

Something along the lines of "# setting the nvt equilibration length to 0.1 ps"

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Added this!

openmm_md/plain_md.ipynb

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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It might be good to give a final look at what files were created (i.e. the output of an ls), and maybe a comment about if you set protocol_repeats to >1 then you will get N full replicates of these outputs?

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Added this!

IAlibay · 2024-03-04T05:50:24Z

openmm_md/plain_md.ipynb

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1)

I'd remove the output from this cell folks might get confused as to why it's CPU only :P

2)

[enhancement]

You could possibly add a "performance consideration" section - something along the lines of "if you're running gas phase, then we suggest setting OPENMM_CPU_THREADS to 1".

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Added this!

IAlibay

Thanks so much for working on this @hannahbaumann !

I've added some comments via reviewnb (it's an app that sits on top of github to help augment jupyter notebook reviews). If you click on the Reply via ReviewNB link then it'll take you to a place where you can more easily review comments.

Anything that's tagged [enhancement] is me saying "this would be nice to have but not an obligation if you don't want to think about it here".

RiesBen · 2024-03-04T17:31:40Z

openmm_md/plain_md.ipynb

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Optional: can we add a simple complex picture here?
I could make one for you :)

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Oh yes, that would be great if you can make a pretty picture for this!

Thank you, this looks great!

RiesBen · 2024-03-04T17:31:40Z

openmm_md/plain_md.ipynb

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short comment on: why is this useful? what can it be used for?
Maybe you only want to see quickly the dynamics of a system.
or want to pre equilibrate a given complex in order to use it for FEs later.

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RiesBen · 2024-03-04T17:31:40Z

openmm_md/plain_md.ipynb

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+{


Line #1. transformation = openfe.Transformation(

could we use a NonTransformation gufe class here?
That way we could get rid of SystemB :)

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https://github.com/OpenFreeEnergy/gufe/blob/45273645f99aaea1ac748854496f076bbabbfeab/gufe/transformations/transformation.py#L243-L259

Thank you, I changed this!

RiesBen · 2024-03-04T17:32:55Z

Hi @hannahbaumann this is a really cool PR, I like it a lot!

I will try it out know directly on my machine and let you know how things go :)

review-notebook-app · 2024-03-04T22:58:16Z

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IAlibay · 2024-03-05T20:38:19Z

openmm_md/plain_md.ipynb

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+{


This doesn't seem to be rendering properly on my end - are you getting the same thing?

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This is what it looks like for me! Is it different for you?

Yeah it's showing as a broken table on preview (by comparison the showcase notebook looks fine).

The second table now looks fine after your latest commit though!

Quick test in #116 - looks like the table is missing a | at the end of each row starting from the third row? Adding those in makes the render work.

IAlibay

Thanks for addressing all the comments!

Only thing left on my end is that the tables don't seem to render properly - I'm not sure if it's just me though.

Just testing table stuff - please ignore

hannahbaumann · 2024-03-07T23:38:38Z

Merged in your fix of the table!

hannahbaumann · 2024-03-07T23:41:37Z

Only thing missing would be a pretty complex picture, if @RiesBen you have one, it would be great if you can add it, but this is something that would be nice to have but not required for merging.

a complex picture :)

testing adding the complex image

IAlibay · 2024-03-22T16:21:13Z

@mikemhenry do you have any idea what's going on with that container build step?

IAlibay · 2024-03-27T11:11:15Z

@richardjgowers you are assigned here - can we go ahead and merge this so we can resolve OpenFreeEnergy/openfe#781?

Add plain MD tutorial

08fa3f0

Change loc MD tutorial

d2afb22

RiesBen self-requested a review February 21, 2024 12:20

RiesBen added the enhancement New feature or request label Feb 21, 2024

hannahbaumann added 2 commits March 1, 2024 14:59

Add openfe quickrun explanation

b0a429d

small fix

5abd063

IAlibay closed this Mar 4, 2024

IAlibay reopened this Mar 4, 2024

IAlibay reviewed Mar 4, 2024

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IAlibay requested changes Mar 4, 2024

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IAlibay mentioned this pull request Mar 4, 2024

Add NonTransformation to top level __init__.py OpenFreeEnergy/openfe#754

Merged

2 tasks

RiesBen reviewed Mar 4, 2024

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changes addressing review comments

508fff1

small fixes

673c80b

IAlibay reviewed Mar 5, 2024

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IAlibay approved these changes Mar 5, 2024

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hannahbaumann and others added 3 commits March 5, 2024 13:55

small fixes

7acd3de

Update plain_md.ipynb

1ab80eb

Merge pull request #116 from OpenFreeEnergy/test-table

8a519b6

Just testing table stuff - please ignore

RiesBen added 3 commits March 22, 2024 16:24

Add files via upload

f9b3e6a

a complex picture :)

Update plain_md.ipynb

9788b9e

testing adding the complex image

Update plain_md.ipynb

da1a8bb

richardjgowers self-assigned this Mar 25, 2024

richardjgowers approved these changes Mar 27, 2024

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richardjgowers merged commit 60e9636 into main Mar 27, 2024
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richardjgowers deleted the md_cookbook branch March 27, 2024 14:11

Add tutorial for MD simulations #97

Add tutorial for MD simulations #97

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hannahbaumann commented Feb 16, 2024

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hannahbaumann commented Mar 7, 2024

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