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OpenMMSolvation: Support for non-cubic boxes and defined box properties #673

Merged
merged 41 commits into from
Aug 27, 2024
Merged

OpenMMSolvation: Support for non-cubic boxes and defined box properties #673

merged 41 commits into from
Aug 27, 2024

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IAlibay
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@IAlibay IAlibay commented Dec 29, 2023 •
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Fixes #585

In this PR:

  • Allows for defining the additional openmm keywords to addSolvent
  • New OpenMM solvation settings + docstring

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pep8speaks commented Dec 29, 2023 •
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Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 690:1: W293 blank line contains whitespace

Line 15:80: E501 line too long (83 > 79 characters)
Line 112:80: E501 line too long (80 > 79 characters)
Line 141:80: E501 line too long (139 > 79 characters)

Line 90:42: E225 missing whitespace around operator

Line 453:9: E128 continuation line under-indented for visual indent
Line 473:34: E251 unexpected spaces around keyword / parameter equals
Line 473:36: E251 unexpected spaces around keyword / parameter equals

Comment last updated at 2024-08-27 13:21:57 UTC

@IAlibay IAlibay changed the title Update system creation for new solvent component options Update solvation settings for non-cubic boxes, etc... Jan 29, 2024
@richardjgowers richardjgowers added this to the 1.0.0 milestone Jan 30, 2024
@IAlibay IAlibay mentioned this pull request Jan 30, 2024
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@IAlibay IAlibay changed the title Update solvation settings for non-cubic boxes, etc... OpenMMSolvation: Support for non-cubic boxes and defined box properties Feb 1, 2024
IAlibay
IAlibay commented Feb 1, 2024
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environment.yml Outdated
@@ -26,6 +26,7 @@ dependencies:
- click
- typing-extensions
- lomap2>=2.3.0
- openmm>=8.0.0
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These solvation settings need OpenMM 8.0. Overall supporting multiple major versions of OpenMM is probably unwise as we'll need to test them all so I would suggest bumping up the minimum version?

Otherwise we can add a version check to the validator.

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IAlibay commented Jul 3, 2024

This is low priority, but it would be amazing if we could get it merged sooner than later.

hannahbaumann
hannahbaumann reviewed Jul 23, 2024
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This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box?

openfe/protocols/openmm_utils/omm_settings.py Outdated Show resolved Hide resolved
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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IAlibay commented Jul 23, 2024

This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box?

I don't think it's a dumb question.

Looks like.. you can't? http://docs.openmm.org/development/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.addSolvent 🙈

I suspect the answer for setting a given density would be to do it manually, selecting a given box size / vectors and then setting the number of waters added manually?

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IAlibay commented Jul 23, 2024

This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box?

I don't think it's a dumb question.

Looks like.. you can't? http://docs.openmm.org/development/api-python/generated/openmm.app.modeller.Modeller.html#openmm.app.modeller.Modeller.addSolvent 🙈

I suspect the answer for setting a given density would be to do it manually, selecting a given box size / vectors and then setting the number of waters added manually?

No... that doesn't work because it's not allowed. Good question indeed.

mikemhenry
mikemhenry approved these changes Jul 24, 2024
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Looks good! Two questions, nothing blocking

environment.yml
@@ -27,7 +27,7 @@ dependencies:
- openfe-analysis>=0.2.0
- click
- typing-extensions
- openmm !=8.1.0
- openmm >=8.0.0,!=8.1.0
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Do we document the min version of OpenMM we support? Or which versions?

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We do not, but we should!

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py
"""
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
settings.solvation_settings.box_shape = 'dodecahedron'
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Should this become our new recommendation? (dodecahedron boxes)

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Long term yes, but we'll need to do some performance benchmarks.

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IAlibay commented Aug 13, 2024

@hannahbaumann if you have time could you have another look at this? I'd like to get to a point where we can merge this but I definitely want your stamp of approval before we do!

@IAlibay IAlibay mentioned this pull request Aug 13, 2024
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hannahbaumann
hannahbaumann approved these changes Aug 15, 2024
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Lgtm, thanks @IAlibay !

@mikemhenry mikemhenry self-requested a review August 15, 2024 22:42
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This could use a changelog entry, otherwise it is good to go!

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IAlibay commented Aug 21, 2024

This could use a changelog entry, otherwise it is good to go!

Good call, done!

@IAlibay IAlibay merged commit 5745e5e into main Aug 27, 2024
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@IAlibay IAlibay deleted the noncubic-solvent branch August 27, 2024 14:00
@IAlibay IAlibay mentioned this pull request Sep 26, 2024
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@mikemhenry mikemhenry mikemhenry approved these changes

@hannahbaumann hannahbaumann hannahbaumann approved these changes

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Solvate with non-cubic boxes
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@IAlibay @pep8speaks @mattwthompson @mikemhenry @hannahbaumann @richardjgowers