Code

Amber support#116

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JohannesKarwou merged 135 commits intomastercbc-univie/transformato:masterfrom amber_supportcbc-univie/transformato:amber_supportCopy head branch name to clipboardJun 5, 2024

+10,807-993

Commits

Commits on Sep 11, 2023

• initial commit toward amber support

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Commits on Sep 18, 2023

• Fix code style issues with Black

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Commits on Nov 6, 2023

• reading in the files works now

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Commits on Nov 7, 2023

• first working example

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• writing amber files

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• option for choosing amber instead of new default charmm

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• adapting the openmm_run skript

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Commits on Nov 8, 2023

• making the submit files easier to read

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• small change in openmm run script

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• test should run now

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• Fix code style issues with Black

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Commits on Nov 9, 2023

• adding the parmed action tools to modify parm7 file on the fly

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• Merge branch 'amber_support' of github.com:wiederm/transformato into amber_support

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Commits on Nov 10, 2023

• creat condition for using the parmed tools action

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• removing unnecessary print statements

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• openmm_run_vacuum.py is not necessary anymore

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• better error handling for unexpected inp files

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• Fix code style issues with Black

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Commits on Nov 14, 2023

• modified analysis for amber FF

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• adapt keyword handling in analysis file

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Commits on Dec 6, 2023

• asfe should work now

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Commits on Dec 11, 2023

• Merge branch 'master' into amber_support

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Commits on Dec 19, 2023

• support pymbar 4

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• Fix code style issues with Black

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Commits on Dec 20, 2023

• Merge branch 'master' into amber_support

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Commits on Jan 11, 2024

• Merge branch 'master' into amber_support

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• handling of vacuum parameters should now be correct

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• Merge branch 'amber_support' of github.com:wiederm/transformato into amber_support

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Commits on Jan 12, 2024

• fixing handling of GPU(CUDA or OpenCL) or CPU

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• Merge branch 'master' into amber_support

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• Update test_amber.py

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• adapt analysis to work with OpenCL

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• Merge branch 'amber_support' of github.com:wiederm/transformato into amber_support

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• reorder handling of gpu, opencl and cpu

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Commits on Jan 18, 2024

• Merge branch 'master' into amber_support

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• Fix code style issues with Black

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• revoke important check

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• Merge branch 'amber_support' of github.com:wiederm/transformato into amber_support

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Commits on Jan 26, 2024

• reading in the two structures

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• Fix code style issues with Black

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Commits on Feb 5, 2024

• first idea to use pdb instead of sdf file

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• Merge branch 'amber_rbfe' of github.com:wiederm/transformato into amber_rbfe

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Commits on Feb 6, 2024

• correct handling of dihedrals when using AMBER

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• small change in mutate file

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• Fix code style issues with Black

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• full test for amber rbfe setup

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Commits on Feb 8, 2024

• complete new idea of handing point mutations

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• Merge branch 'amber_support' into amber_rbfe

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• Fix code style issues with Black

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  e64d466

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• remove unnecessary print statement

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• Merge branch 'amber_rbfe' of github.com:wiederm/transformato into amber_rbfe

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• Merge pull request #124 from cbc-univie/amber_rbfe

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Commits on Feb 20, 2024

• full charmm point mutation support

  JohannesKarwou

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• fixing small bug

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• Fix code style issues with Black

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Commits on Apr 17, 2024

• first test for handling drude ff

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• test statement

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• Fix code style issues with Black

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• ethanol first draft

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• resolve merge conflict

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• Fix code style issues with Black

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Commits on Apr 24, 2024

• lj scaling and lp handling

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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Commits on Apr 30, 2024

• commit "test"

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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Commits on May 3, 2024

• change to IntermediateStateFactory so that LP bonds are included

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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Commits on May 7, 2024

• changes made to enable openmm run on cluster

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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Commits on May 8, 2024

• modfy analysis

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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  8ddce46

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• use better integrator

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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Commits on May 10, 2024

• save prop information as well

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• Update system.py

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• Update CI.yaml

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Commits on May 15, 2024

• Merge pull request #127 from cbc-univie/psf_vac_handling

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• change handling of str file

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• Fix code style issues with Black

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• drude as option in yaml file

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• Fix code style issues with Black

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• working variable

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• bad except statement

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• now working

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• Fix code style issues with Black

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• change path variable

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• option for using drude in yaml file

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• bool instead of str variable

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• use if else statement instead

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• adding flags to vacuum file

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• updated drude openmm run file

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• path change

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• remove dependency of wrapped psf in analysis

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Commits on May 16, 2024

• removed "corr_wrapped" from analysis.py

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• removed "corr_wrapped" from analysis.py

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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Commits on May 21, 2024

• added drude condition to include/exclude unl.str in toppar.str

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• drude condition to include/exclude unl.str

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• Fix code style issues with Black

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• Fix code style issues with Black

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• unl.str trouble #2

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• Fix code style issues with Black

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• unl.str trouble #3

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• unl trouble #4

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• Fix code style issues with Black

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• unl trouble #5

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• Fix code style issues with Black

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• unl #5.2

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• unl trouble 6

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• unl trouble #6

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• Fix code style issues with Black

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Commits on May 27, 2024

• checking self.drude

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• Fix code style issues with Black

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• checking self.drude

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• Merge branch 'drude_dev' of github.com:cbc-univie/transformato into drude_dev

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• another drude check

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• clean up write toppar.str

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Commits on May 29, 2024

• revert to pymbar version 3

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• Fix code style issues with Black

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Commits on Jun 5, 2024

• Delete analysis.py

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• Delete notebooks/toppar_tester.ipynb

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• Delete notebooks/drude_config_test.ipynb

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• Delete notebooks/platform_tester.ipynb

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• Update __init__.py

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• small changes

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• Merge pull request #126 from cbc-univie/drude_dev

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