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OpenFreeEnergy
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openfe-gromacs
Gromacs-based protocols for Open Free Energy
https://openfe-gromacs.readthedocs.io/en/latest/
MIT License
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Test openff-interchange 0.4 rc
#66
mikemhenry
closed
3 weeks ago
2
Test interchange rc
#65
mikemhenry
closed
3 weeks ago
1
[pre-commit.ci] pre-commit autoupdate
#64
pre-commit-ci[bot]
closed
1 month ago
1
Add tests for different charge backends, e.g. NAGL
#63
hannahbaumann
opened
1 month ago
0
Adding single point energy test
#62
hannahbaumann
opened
1 month ago
0
Unpin openff interchange version after new interchange release
#61
hannahbaumann
opened
1 month ago
0
Update README.md
#60
hannahbaumann
closed
1 month ago
1
Fix flake8 errors
#59
mikemhenry
closed
1 month ago
2
Switch to src layout
#58
hannahbaumann
opened
1 month ago
1
Fix the docs title
#57
IAlibay
closed
1 month ago
1
Add link to the docs on the readme (make it a badge?)
#56
IAlibay
closed
1 month ago
1
Expose full settings API in docs
#55
IAlibay
opened
1 month ago
0
Fix docs
#54
IAlibay
closed
1 month ago
1
`mdout.mdp` is being written outside of `shared` and `scratch` directories.
#53
IAlibay
closed
1 month ago
1
`top` and `gro` are unintuitive setting names & locations
#52
IAlibay
opened
1 month ago
0
Switch to a `src` layout style
#51
IAlibay
opened
1 month ago
0
Remove empty "data" directory at the top level.
#50
IAlibay
closed
1 month ago
1
Review engine settings for gmx mdrun
#49
hannahbaumann
opened
1 month ago
0
Add support for virtual sites once they are supported in Interchange
#48
hannahbaumann
opened
1 month ago
0
Move things to utils, test interchange creation
#47
hannahbaumann
closed
1 month ago
2
Add gather and integration test
#46
hannahbaumann
opened
1 month ago
2
Set Interchange experimental env variable in protocol
#45
hannahbaumann
closed
1 month ago
0
Catch and report errors on execution
#44
IAlibay
opened
1 month ago
0
Some protocol updates: MDPs dict, vacuum check
#43
hannahbaumann
closed
1 month ago
2
Removes output files from results if they should not exist
#42
hannahbaumann
closed
1 month ago
2
Add MD protocol integration test
#41
IAlibay
opened
1 month ago
0
Move vacuuum disallowed check to Protocol creation
#40
IAlibay
closed
1 month ago
0
Add gather tests
#39
IAlibay
opened
1 month ago
0
Have MDPs be a dictionary rather than a list of file handles
#38
IAlibay
closed
1 month ago
0
Add tests where you have missing files being message through to `_run_gromacs`
#37
IAlibay
opened
1 month ago
0
Avoid bare asserts (in `_run_gromacs`)
#36
IAlibay
opened
1 month ago
0
Have tests that check that the outputs of the SetupUnit are sensible and expected
#35
IAlibay
opened
1 month ago
0
Remove stub files
#34
IAlibay
closed
1 month ago
1
Add tests for interchange system creation
#33
IAlibay
closed
1 month ago
0
Add tests for MDP writing
#32
IAlibay
opened
1 month ago
0
Move MDP writing to their own utilities
#31
IAlibay
closed
1 month ago
0
Move `create_interchange` and `_assign_partial_charges` to their own utilities
#30
IAlibay
closed
1 month ago
1
Add engine settings for GPU selection and pinning
#29
IAlibay
closed
1 month ago
1
Validate gmx executable + tests
#28
IAlibay
opened
1 month ago
0
Remove filepaths from outputs if the files are not expected to be created
#27
hannahbaumann
closed
1 month ago
0
Get read the docs page up and running
#26
hannahbaumann
closed
1 month ago
0
Write documentation for the Gromacs MD protocol
#25
hannahbaumann
closed
1 month ago
0
Add a test to make sure atom names are passed properly when writing out the Interchange object
#24
hannahbaumann
closed
1 month ago
0
Remove OpenMMEngineSettings and create GromacsEngineSettings
#23
hannahbaumann
closed
1 month ago
4
Example notebook for Gromacs MD simulations
#22
hannahbaumann
closed
1 month ago
4
Write alternate `GromacsMDRunUnit` that used the `gmxapi` instead of subprocess
#21
hannahbaumann
opened
1 month ago
0
We need `integrator_settings` for creating the OpenMM system, but they may confuse the user as they are not used in the simulations
#20
hannahbaumann
opened
1 month ago
1
`engine_settings` should be removed as they are OpenMM specific
#19
hannahbaumann
closed
1 month ago
0
Write example notebook
#17
hannahbaumann
closed
1 month ago
0
Test saving of a protein containing .gro file from Interchange
#16
hannahbaumann
closed
1 month ago
1
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