Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Protocol to run plain MD simulations #516

Merged
merged 78 commits into from
Dec 28, 2023
Merged

Protocol to run plain MD simulations #516

merged 78 commits into from
Dec 28, 2023

Commits on Jul 31, 2023

  1. start plain MD scripts

    @hannahbaumann
    hannahbaumann committed Jul 31, 2023
    Configuration menu
    Copy the full SHA
    1610300 View commit details
    Browse the repository at this point in the history

Commits on Aug 1, 2023

  1. Add tests, fixing some errors in methods

    @hannahbaumann
    hannahbaumann committed Aug 1, 2023
    Configuration menu
    Copy the full SHA
    e64fb75 View commit details
    Browse the repository at this point in the history

Commits on Aug 2, 2023

  1. Add gathertest

    @hannahbaumann
    hannahbaumann committed Aug 2, 2023
    Configuration menu
    Copy the full SHA
    86a60c9 View commit details
    Browse the repository at this point in the history

  2. Add StateDataReporter

    @hannahbaumann
    hannahbaumann committed Aug 2, 2023
    Configuration menu
    Copy the full SHA
    b9c8413 View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2023

  1. Cleanup functions

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    f33e21d View commit details
    Browse the repository at this point in the history

  2. fix integrator units

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    72ee364 View commit details
    Browse the repository at this point in the history

  3. fix setvelocity unit

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    1516300 View commit details
    Browse the repository at this point in the history

  4. test reporter

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    b9f9b6d View commit details
    Browse the repository at this point in the history

  5. change reporter to xtc

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    033a9ac View commit details
    Browse the repository at this point in the history

  6. change reporter to dcd

    @hannahbaumann
    hannahbaumann committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    3901dfa View commit details
    Browse the repository at this point in the history

Commits on Aug 4, 2023

  1. clean up reporters

    @hannahbaumann
    hannahbaumann committed Aug 4, 2023
    Configuration menu
    Copy the full SHA
    dbcacf3 View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2023

  1. Add checkpoint reporter

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    7b4c04d View commit details
    Browse the repository at this point in the history

  2. change reporter to xtc

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    95b9c16 View commit details
    Browse the repository at this point in the history

  3. Fix reporters

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    96b69f0 View commit details
    Browse the repository at this point in the history

  4. Fix StateReporter

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    fca9c23 View commit details
    Browse the repository at this point in the history

  5. Add output indices traj and other fixes

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    48b626c View commit details
    Browse the repository at this point in the history

  6. merge changes

    @hannahbaumann
    hannahbaumann committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    ed79587 View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2023

  1. Merge branch 'main' into plain_md

    @hannahbaumann
    hannahbaumann authored Aug 8, 2023
    Configuration menu
    Copy the full SHA
    ac15045 View commit details
    Browse the repository at this point in the history

  2. changes test

    @hannahbaumann
    hannahbaumann committed Aug 8, 2023
    Configuration menu
    Copy the full SHA
    0b61cbf View commit details
    Browse the repository at this point in the history

Commits on Aug 15, 2023

  1. Merge branch 'main' into plain_md

    @hannahbaumann
    hannahbaumann authored Aug 15, 2023
    Configuration menu
    Copy the full SHA
    559d18d View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2023

  1. style_fix 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
    @hannahbaumann @IAlibay
    hannahbaumann and IAlibay authored Nov 3, 2023
    Configuration menu
    Copy the full SHA
    e77cad6 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i… 

    …nto plain_md
    @hannahbaumann
    hannahbaumann committed Nov 3, 2023
    Configuration menu
    Copy the full SHA
    3b0f212 View commit details
    Browse the repository at this point in the history

Commits on Nov 6, 2023

  1. remove preequil

    @hannahbaumann
    hannahbaumann committed Nov 6, 2023
    Configuration menu
    Copy the full SHA
    e0ea862 View commit details
    Browse the repository at this point in the history

Commits on Nov 8, 2023

  1. Change system name

    @hannahbaumann
    hannahbaumann committed Nov 8, 2023
    Configuration menu
    Copy the full SHA
    4b52c25 View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2023

  1. Save pdb of the system and of minimized structure

    @hannahbaumann
    hannahbaumann committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    8338cf3 View commit details
    Browse the repository at this point in the history

Commits on Nov 14, 2023

  1. Fixes plain MD method

    @hannahbaumann
    hannahbaumann committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    9c74b84 View commit details
    Browse the repository at this point in the history

Commits on Nov 17, 2023

  1. Fix docstring

    @hannahbaumann
    hannahbaumann committed Nov 17, 2023
    Configuration menu
    Copy the full SHA
    3ff34e2 View commit details
    Browse the repository at this point in the history

  2. Add ffcache test

    @hannahbaumann
    hannahbaumann committed Nov 17, 2023
    Configuration menu
    Copy the full SHA
    22eec31 View commit details
    Browse the repository at this point in the history

Commits on Nov 20, 2023

  1. Add NVT and NPT equilibration

    @hannahbaumann
    hannahbaumann committed Nov 20, 2023
    Configuration menu
    Copy the full SHA
    e160600 View commit details
    Browse the repository at this point in the history

  2. Fix equilbration settings

    @hannahbaumann
    hannahbaumann committed Nov 20, 2023
    Configuration menu
    Copy the full SHA
    24d5a2f View commit details
    Browse the repository at this point in the history

  3. Change get_simsteps to handle NVT equilibration

    @hannahbaumann
    hannahbaumann committed Nov 20, 2023
    Configuration menu
    Copy the full SHA
    0c66327 View commit details
    Browse the repository at this point in the history

  4. Fix positions for pdb storage

    @hannahbaumann
    hannahbaumann committed Nov 20, 2023
    Configuration menu
    Copy the full SHA
    df7f921 View commit details
    Browse the repository at this point in the history

Commits on Nov 21, 2023

  1. Fix get_simsteps tests

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    a51def2 View commit details
    Browse the repository at this point in the history

  2. Disable barostat for NVT equilibration, bring it back for NPT

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    c5f5667 View commit details
    Browse the repository at this point in the history

  3. Output pdb file after NVT equilibration and after NPT equilibration

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    2f586a9 View commit details
    Browse the repository at this point in the history

  4. Add without_oechem_backend wrapper

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    9170413 View commit details
    Browse the repository at this point in the history

  5. Add log_system_probe

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    b33bc7a View commit details
    Browse the repository at this point in the history

  6. Add verbosity flag

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    8049534 View commit details
    Browse the repository at this point in the history

  7. Small fixes

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    97171dc View commit details
    Browse the repository at this point in the history

  8. Pep8 fixes

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    b3bb0eb View commit details
    Browse the repository at this point in the history

  9. Change system naming

    @hannahbaumann
    hannahbaumann committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    d0fbe97 View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2023

  1. Move actual MD stuff into separate function to be used in other proto… 

    …cols
    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    4fbf74f View commit details
    Browse the repository at this point in the history

  2. Small fixes

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    323f1e8 View commit details
    Browse the repository at this point in the history

  3. Add benzene_modifications

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    40978e4 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'main' into plain_md

    @hannahbaumann
    hannahbaumann authored Nov 22, 2023
    Configuration menu
    Copy the full SHA
    e5c470b View commit details
    Browse the repository at this point in the history

  5. Remove benzene_modifications

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    1507305 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i… 

    …nto plain_md
    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    be8c4f2 View commit details
    Browse the repository at this point in the history

  7. Change to smc_components

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    8cffa42 View commit details
    Browse the repository at this point in the history

  8. Move repeat_settings to protocol

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    c119917 View commit details
    Browse the repository at this point in the history

  9. Change from equ_x to equil_x

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    11ff8ca View commit details
    Browse the repository at this point in the history

  10. Change comp_type

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    9473a96 View commit details
    Browse the repository at this point in the history

  11. Remove stateB from ProtocolUnit

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    b63ae2a View commit details
    Browse the repository at this point in the history

  12. Use individual settings for _run_MD function

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    db4a847 View commit details
    Browse the repository at this point in the history

  13. Small fix

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    0d527e0 View commit details
    Browse the repository at this point in the history

  14. Merge branch 'main' into plain_md

    @hannahbaumann
    hannahbaumann authored Nov 22, 2023
    Configuration menu
    Copy the full SHA
    7ed3f5d View commit details
    Browse the repository at this point in the history

  15. Fix npt issue

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    98aa2ba View commit details
    Browse the repository at this point in the history

  16. Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i… 

    …nto plain_md
    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    8d186ac View commit details
    Browse the repository at this point in the history

  17. small fix

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    8aa64a6 View commit details
    Browse the repository at this point in the history

  18. small fix2

    @hannahbaumann
    hannahbaumann committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    5b9b572 View commit details
    Browse the repository at this point in the history

  19. Add init files

    @IAlibay
    IAlibay committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    45890d4 View commit details
    Browse the repository at this point in the history

Commits on Nov 23, 2023

  1. Merge branch 'main' into plain_md

    @hannahbaumann
    hannahbaumann authored Nov 23, 2023
    Configuration menu
    Copy the full SHA
    ed0c5b5 View commit details
    Browse the repository at this point in the history

  2. Add test for result json file

    @hannahbaumann
    hannahbaumann committed Nov 23, 2023
    Configuration menu
    Copy the full SHA
    3996e37 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'plain_md' of https://github.com/OpenFreeEnergy/openfe i… 

    …nto plain_md
    @hannahbaumann
    hannahbaumann committed Nov 23, 2023
    Configuration menu
    Copy the full SHA
    eca1b01 View commit details
    Browse the repository at this point in the history

  4. Add results json files for MD run

    @hannahbaumann
    hannahbaumann committed Nov 23, 2023
    Configuration menu
    Copy the full SHA
    27b9b42 View commit details
    Browse the repository at this point in the history

  5. Add tests for logging output

    @hannahbaumann
    hannahbaumann committed Nov 23, 2023
    Configuration menu
    Copy the full SHA
    2d6e38e View commit details
    Browse the repository at this point in the history

  6. Merge branch 'main' into plain_md

    @IAlibay
    IAlibay authored Nov 23, 2023
    Configuration menu
    Copy the full SHA
    552e31b View commit details
    Browse the repository at this point in the history

Commits on Nov 24, 2023

  1. Changes __init__.py

    @hannahbaumann
    hannahbaumann committed Nov 24, 2023
    Configuration menu
    Copy the full SHA
    f5e6d99 View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2023

  1. add return annotation for results

    @hannahbaumann
    hannahbaumann committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    146b8d5 View commit details
    Browse the repository at this point in the history

  2. Update openfe/protocols/openmm_md/plain_md_methods.py 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
    @hannahbaumann @IAlibay
    hannahbaumann and IAlibay authored Dec 7, 2023
    Configuration menu
    Copy the full SHA
    71f09d1 View commit details
    Browse the repository at this point in the history

  3. make settings names more specific

    @hannahbaumann
    hannahbaumann committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    085919d View commit details
    Browse the repository at this point in the history

Commits on Dec 8, 2023

  1. change results.json file with new settings names

    @hannahbaumann
    hannahbaumann committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    f21a7b1 View commit details
    Browse the repository at this point in the history

  2. change run method to take temp and barostat_frequency instead of full… 

    … settings
    @hannahbaumann
    hannahbaumann committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    7f46b7f View commit details
    Browse the repository at this point in the history

  3. add slow test

    @hannahbaumann
    hannahbaumann committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    f8ec471 View commit details
    Browse the repository at this point in the history

  4. fix test

    @hannahbaumann
    hannahbaumann committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    39803e5 View commit details
    Browse the repository at this point in the history

Commits on Dec 12, 2023

  1. Update openfe/protocols/openmm_md/plain_md_methods.py 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
    @hannahbaumann @IAlibay
    hannahbaumann and IAlibay authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    b9c924b View commit details
    Browse the repository at this point in the history

  2. Change purepath to path

    @hannahbaumann
    hannahbaumann committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    4704336 View commit details
    Browse the repository at this point in the history

Commits on Dec 13, 2023

  1. Change PurePath to Path

    @hannahbaumann
    hannahbaumann committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    64109d8 View commit details
    Browse the repository at this point in the history

Commits on Dec 28, 2023

  1. Merge branch 'main' into plain_md

    @IAlibay
    IAlibay authored Dec 28, 2023
    Configuration menu
    Copy the full SHA
    b16d91d View commit details
    Browse the repository at this point in the history