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Amber support #116

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merged 135 commits into from
Jun 5, 2024
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abf23ab
initial commit toward amber support
JohannesKarwou Sep 11, 2023
d02e02b
Fix code style issues with Black
lint-action Sep 18, 2023
2fe27e6
reading in the files works now
JohannesKarwou Nov 6, 2023
944ab7a
first working example
JohannesKarwou Nov 7, 2023
c5eab29
writing amber files
JohannesKarwou Nov 7, 2023
9c38526
option for choosing amber instead of new default charmm
JohannesKarwou Nov 7, 2023
d461e10
adapting the openmm_run skript
JohannesKarwou Nov 7, 2023
ddbcf81
making the submit files easier to read
JohannesKarwou Nov 8, 2023
7a13d0b
small change in openmm run script
JohannesKarwou Nov 8, 2023
5bca575
test should run now
JohannesKarwou Nov 8, 2023
ef36dc1
Fix code style issues with Black
lint-action Nov 8, 2023
f6fb152
adding the parmed action tools to modify parm7 file on the fly
JohannesKarwou Nov 9, 2023
6d0187a
Merge branch 'amber_support' of github.com:wiederm/transformato into …
JohannesKarwou Nov 9, 2023
64bb2e5
creat condition for using the parmed tools action
JohannesKarwou Nov 10, 2023
763f539
removing unnecessary print statements
JohannesKarwou Nov 10, 2023
72c1eda
openmm_run_vacuum.py is not necessary anymore
JohannesKarwou Nov 10, 2023
2d1c701
better error handling for unexpected inp files
JohannesKarwou Nov 10, 2023
87a22a9
Fix code style issues with Black
lint-action Nov 10, 2023
7d194ea
modified analysis for amber FF
JohannesKarwou Nov 14, 2023
f51e3d1
adapt keyword handling in analysis file
JohannesKarwou Nov 14, 2023
64bf600
asfe should work now
JohannesKarwou Dec 6, 2023
b6e42f4
Merge branch 'master' into amber_support
JohannesKarwou Dec 11, 2023
8f854c7
support pymbar 4
JohannesKarwou Dec 19, 2023
ed6bf26
Fix code style issues with Black
lint-action Dec 19, 2023
c4dcd79
Merge branch 'master' into amber_support
JohannesKarwou Dec 20, 2023
9e5253e
Merge branch 'master' into amber_support
JohannesKarwou Jan 11, 2024
618e51e
handling of vacuum parameters should now be correct
JohannesKarwou Jan 11, 2024
27aa374
Merge branch 'amber_support' of github.com:wiederm/transformato into …
JohannesKarwou Jan 11, 2024
4d0bd68
fixing handling of GPU(CUDA or OpenCL) or CPU
JohannesKarwou Jan 12, 2024
4eae819
Merge branch 'master' into amber_support
JohannesKarwou Jan 12, 2024
de0b430
Update test_amber.py
JohannesKarwou Jan 12, 2024
79b483c
adapt analysis to work with OpenCL
JohannesKarwou Jan 12, 2024
f8f063d
Merge branch 'amber_support' of github.com:wiederm/transformato into …
JohannesKarwou Jan 12, 2024
0ed0924
reorder handling of gpu, opencl and cpu
JohannesKarwou Jan 12, 2024
226361e
Merge branch 'master' into amber_support
JohannesKarwou Jan 18, 2024
52c02fe
Fix code style issues with Black
lint-action Jan 18, 2024
e024ac8
revoke important check
JohannesKarwou Jan 18, 2024
138b013
Merge branch 'amber_support' of github.com:wiederm/transformato into …
JohannesKarwou Jan 18, 2024
a55ed93
reading in the two structures
JohannesKarwou Jan 26, 2024
31ca40c
Fix code style issues with Black
lint-action Jan 26, 2024
f9ca768
first idea to use pdb instead of sdf file
JohannesKarwou Feb 5, 2024
cd72c99
Merge branch 'amber_rbfe' of github.com:wiederm/transformato into amb…
JohannesKarwou Feb 5, 2024
9117fac
correct handling of dihedrals when using AMBER
JohannesKarwou Feb 6, 2024
5cf90ae
small change in mutate file
JohannesKarwou Feb 6, 2024
c8e9146
Fix code style issues with Black
lint-action Feb 6, 2024
889ebef
full test for amber rbfe setup
JohannesKarwou Feb 6, 2024
a7aef86
complete new idea of handing point mutations
JohannesKarwou Feb 8, 2024
cd771d6
Merge branch 'amber_support' into amber_rbfe
JohannesKarwou Feb 8, 2024
e64d466
Fix code style issues with Black
lint-action Feb 8, 2024
05b0685
remove unnecessary print statement
JohannesKarwou Feb 8, 2024
ca20656
Merge branch 'amber_rbfe' of github.com:wiederm/transformato into amb…
JohannesKarwou Feb 8, 2024
00db6a9
Merge pull request #124 from cbc-univie/amber_rbfe
JohannesKarwou Feb 8, 2024
71c7e17
full charmm point mutation support
JohannesKarwou Feb 20, 2024
2c4fc59
fixing small bug
JohannesKarwou Feb 20, 2024
5688467
Fix code style issues with Black
lint-action Feb 20, 2024
1f37a9a
first test for handling drude ff
loeflerm Apr 17, 2024
2da46c8
test statement
loeflerm Apr 17, 2024
769eb84
Fix code style issues with Black
lint-action Apr 17, 2024
ad494c2
ethanol first draft
loeflerm Apr 17, 2024
315dca7
resolve merge conflict
loeflerm Apr 17, 2024
355dade
Fix code style issues with Black
lint-action Apr 17, 2024
1f45839
lj scaling and lp handling
loeflerm Apr 24, 2024
525a17e
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm Apr 24, 2024
4d403c0
Fix code style issues with Black
lint-action Apr 24, 2024
e0d1aa8
commit "test"
loeflerm Apr 30, 2024
6dcda59
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm Apr 30, 2024
d8c8b7b
Fix code style issues with Black
lint-action Apr 30, 2024
7facf95
change to IntermediateStateFactory so that LP bonds are included
loeflerm May 3, 2024
8253cd8
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 3, 2024
eea2875
Fix code style issues with Black
lint-action May 3, 2024
c38ae44
changes made to enable openmm run on cluster
loeflerm May 7, 2024
ebc438b
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 7, 2024
ba2caea
Fix code style issues with Black
lint-action May 7, 2024
0acabec
modfy analysis
loeflerm May 8, 2024
047e78d
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 8, 2024
8ddce46
Fix code style issues with Black
lint-action May 8, 2024
ea96097
use better integrator
loeflerm May 8, 2024
6c7120e
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 8, 2024
b9e7920
save prop information as well
JohannesKarwou May 10, 2024
aec63c4
Update system.py
JohannesKarwou May 10, 2024
75ac3a0
Update CI.yaml
JohannesKarwou May 10, 2024
f216777
Merge pull request #127 from cbc-univie/psf_vac_handling
JohannesKarwou May 15, 2024
69dc377
change handling of str file
JohannesKarwou May 15, 2024
a68ce8f
Fix code style issues with Black
lint-action May 15, 2024
88ac4d4
drude as option in yaml file
JohannesKarwou May 15, 2024
3317b12
Fix code style issues with Black
lint-action May 15, 2024
e513fd4
working variable
JohannesKarwou May 15, 2024
17687b2
bad except statement
JohannesKarwou May 15, 2024
0ca9f15
now working
JohannesKarwou May 15, 2024
cdfc7bf
Fix code style issues with Black
lint-action May 15, 2024
e8bbe2b
change path variable
JohannesKarwou May 15, 2024
0226002
option for using drude in yaml file
JohannesKarwou May 15, 2024
c379fcc
bool instead of str variable
JohannesKarwou May 15, 2024
a326aef
use if else statement instead
JohannesKarwou May 15, 2024
67e5b75
adding flags to vacuum file
JohannesKarwou May 15, 2024
199cc1f
updated drude openmm run file
JohannesKarwou May 15, 2024
15f2942
path change
loeflerm May 15, 2024
3871add
remove dependency of wrapped psf in analysis
JohannesKarwou May 15, 2024
7820d42
removed "corr_wrapped" from analysis.py
loeflerm May 16, 2024
e925bf7
removed "corr_wrapped" from analysis.py
loeflerm May 16, 2024
1ddb15a
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 16, 2024
44dbd3f
Fix code style issues with Black
lint-action May 16, 2024
08accb2
added drude condition to include/exclude unl.str in toppar.str
loeflerm May 21, 2024
58abfef
drude condition to include/exclude unl.str
loeflerm May 21, 2024
62ad373
Fix code style issues with Black
lint-action May 21, 2024
ca4c075
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 21, 2024
83672e1
Fix code style issues with Black
lint-action May 21, 2024
73c8605
unl.str trouble #2
loeflerm May 21, 2024
e58b6e9
Fix code style issues with Black
lint-action May 21, 2024
62d3bd9
unl.str trouble #3
loeflerm May 21, 2024
b829883
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 21, 2024
43640f4
unl trouble #4
loeflerm May 21, 2024
36452a5
Fix code style issues with Black
lint-action May 21, 2024
aa130e2
unl trouble #5
loeflerm May 21, 2024
efed66d
Fix code style issues with Black
lint-action May 21, 2024
e801060
unl #5.2
loeflerm May 21, 2024
83ebd18
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 21, 2024
fb623ff
unl trouble 6
loeflerm May 21, 2024
2d2d885
unl trouble #6
loeflerm May 21, 2024
33667b5
Fix code style issues with Black
lint-action May 21, 2024
9a6a7aa
checking self.drude
loeflerm May 27, 2024
c6414db
Fix code style issues with Black
lint-action May 27, 2024
e4aa898
checking self.drude
loeflerm May 27, 2024
1f15971
Merge branch 'drude_dev' of github.com:cbc-univie/transformato into d…
loeflerm May 27, 2024
963407b
another drude check
loeflerm May 27, 2024
6006750
clean up write toppar.str
loeflerm May 27, 2024
fda3d7d
revert to pymbar version 3
loeflerm May 29, 2024
82d5e39
Fix code style issues with Black
lint-action May 29, 2024
c048863
Delete analysis.py
JohannesKarwou Jun 5, 2024
3bbb639
Delete notebooks/toppar_tester.ipynb
JohannesKarwou Jun 5, 2024
f86fa60
Delete notebooks/drude_config_test.ipynb
JohannesKarwou Jun 5, 2024
3569864
Delete notebooks/platform_tester.ipynb
JohannesKarwou Jun 5, 2024
e65d887
Update __init__.py
JohannesKarwou Jun 5, 2024
68ae85a
small changes
JohannesKarwou Jun 5, 2024
6212fd3
Merge pull request #126 from cbc-univie/drude_dev
JohannesKarwou Jun 5, 2024
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1 change: 1 addition & 0 deletions .gitattributes
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# Apply override to all files in the directory (source: https://github.com/github/linguist/blob/master/docs/overrides.md)
data/** linguist-vendored
transformato/toppar/** linguist-vendored
transformato/_version.py export-subst
6 changes: 2 additions & 4 deletions .github/workflows/CI.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,10 @@ on:
# Both are tracked here to keep legacy and new codes working
push:
branches:
- "master"
- "main"
- '**'
pull_request:
branches:
- "master"
- "main"
- '**'
schedule:
# Nightly tests run on master by default:
# Scheduled workflows run on the latest commit on the default or base branch.
Expand Down
2 changes: 1 addition & 1 deletion devtools/conda-envs/fep_env.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ dependencies:
- openmmtools
- numpy
- ipython
- pymbar
- pymbar=3
- rdkit
- parmed
- pyyaml
Expand Down
7 changes: 7 additions & 0 deletions transformato/.vscode/settings.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
{
"python.testing.pytestArgs": [
"."
],
"python.testing.unittestEnabled": false,
"python.testing.pytestEnabled": true
}
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