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quick fix openm install and 8.2 version #1145

Merged
merged 23 commits into from
Dec 16, 2024
Merged

quick fix openm install and 8.2 version #1145

merged 23 commits into from
Dec 16, 2024

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VGPReys
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@VGPReys VGPReys commented Nov 14, 2024 •
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Checklist

  • Tests added for the new code
  • Documentation added for the code changes
  • Does not break licensing
  • Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

  • Update OpenMM installation instructions
  • Small modification of the code to make sure implicit solvent still functional
  • Adding custom solution for chain break detection: It has been observed that chain breaks in the OpenMM module are making the simulation crash. Therefore we are now pre-processing the input files in the search of such breaks and adding TER statements between them, allowing to run the simulation without issues.

Related Issue

Closes #1144
Closes #1153

@VGPReys VGPReys self-assigned this Nov 14, 2024
@VGPReys VGPReys added the m|openmm Module to work with OpenMM label Nov 14, 2024
@VGPReys VGPReys requested review from mgiulini and a team November 18, 2024 09:25
amjjbonvin
amjjbonvin reviewed Nov 18, 2024
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VGPReys
VGPReys commented Nov 18, 2024
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mgiulini
mgiulini previously approved these changes Nov 18, 2024
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amjjbonvin
amjjbonvin reviewed Nov 18, 2024
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amjjbonvin commented Nov 18, 2024 via email

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VGPReys commented Nov 19, 2024

More complicated than what I thought...
conda-forge and pip do not behave the same.
deposited versions are not the same.
Something functional with conda is not with venv and vice-versa...
I am about to have two different installation instructions, depending on how haddock3 is installed.
Also they are constantly providing updates on their side...

@VGPReys VGPReys mentioned this pull request Nov 19, 2024
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@rvhonorato
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rvhonorato commented Nov 19, 2024 •
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More complicated than what I thought... conda-forge and pip do not behave the same. deposited versions are not the same. Something functional with conda is not with venv and vice-versa... I am about to have two different installation instructions, depending on how haddock3 is installed. Also they are constantly providing updates on their side...

It's 8.2 on both of them, your instructions are wrong - not the providers, you need to fix the version.

pip install openmm==8.2.0

conda install -c conda-forge openmm==8.2.0

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I know you like to do things on trial-and-error instead of reading the documentation first, so just in case you have not yet spent some time trying to figure out with which version openmm 8.2 is compatible, you can find this information either in the package info on conda-forge (https://anaconda.org/conda-forge/openmm/files/modal/info/672eb96e41d1a787229656f8) or on pypi

VGPReys
VGPReys commented Nov 19, 2024
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VGPReys commented Nov 19, 2024

Indeed good idea to specify the version/tag.

But I still do not understand why under conda I manage to install it with python3.9 and not for venv pip...

VGPReys and others added 11 commits November 21, 2024 17:51
@VGPReys
reduce solvant equilibration timesteps in -test.cfg
a25cf3a
@VGPReys
Upgrade on the openmm module
20dc03d 
- [X] Inceasing temperature coupling to reach faster queried temperature
- [X] Adding pdb_tidy pre-processing step to detect chain breaks
- [ ] May require additional pre-processing steps to detect chain breaks if no shift in residue numbering...
@VGPReys
manage automatic detection of chain breaks as preprocessing step in o…
a94a5c4 
…penmm
@VGPReys
adding test comparison files
97fa61a
@VGPReys
test for chain break functionality
21603ee
@VGPReys
modify openmm pre-processing steps to use chain break detection
a2ab9dd
@VGPReys
adding chain break detection function in libpdb
631d4b4
@VGPReys
removing unused pdbtidy from openmm
9d52aac
@VGPReys
fix last residue writing
7ca3a76
@VGPReys
Merge branch 'main' into openmm-8-2-updates
4489fce
@VGPReys
Merge branch 'main' into openmm-8-2-updates
a653ff6
@VGPReys VGPReys requested a review from a team December 5, 2024 15:55
@VGPReys VGPReys enabled auto-merge December 16, 2024 11:11
@VGPReys VGPReys merged commit 5df3836 into main Dec 16, 2024
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@VGPReys VGPReys deleted the openmm-8-2-updates branch December 16, 2024 11:27
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