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basic idea for templates to create permutations of possible donor / acceptor H sites #103

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basic idea for templates to create permutations of possible donor / acceptor H sites #103

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Commits on May 31, 2023

  1. donor/acceptor structure for Hs in templates

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Commits on Jun 1, 2023

  1. fixed tests

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  3. Merge pull request #102 from florianjoerg/customnonbondedforce 

    CustomNonbondedForce
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Commits on Jun 5, 2023

  1. Merge branch 'main' into tetr_marta

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Jun 19, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/asottile/pyupgrade: v3.4.0 → v3.7.0](asottile/pyupgrade@v3.4.0...v3.7.0)
- [github.com/charliermarsh/ruff-pre-commit: v0.0.270 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.270...v0.0.272)
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Commits on Jun 23, 2023

  1. Merge pull request #105 from florianjoerg/pre-commit-ci-update-config

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Commits on Jun 26, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)
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Commits on Jun 27, 2023

  1. Merge pull request #106 from florianjoerg/pre-commit-ci-update-config 

    ⬆ [pre-commit.ci] pre-commit autoupdate
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Commits on Jun 29, 2023

  1. deleted unnecessary lines

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  2. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Jul 3, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/asottile/pyupgrade: v3.7.0 → v3.8.0](asottile/pyupgrade@v3.7.0...v3.8.0)
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  2. Merge pull request #108 from florianjoerg/pre-commit-ci-update-config 

    ⬆ [pre-commit.ci] pre-commit autoupdate
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Commits on Aug 7, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/asottile/pyupgrade: v3.8.0 → v3.10.1](asottile/pyupgrade@v3.8.0...v3.10.1)
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.275...v0.0.282)
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Commits on Aug 13, 2023

  1. Merge pull request #109 from florianjoerg/pre-commit-ci-update-config

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Commits on Aug 14, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)
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Commits on Aug 18, 2023

  1. started tests for toh2 system

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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  3. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Aug 21, 2023

  1. Merge pull request #110 from florianjoerg/pre-commit-ci-update-config 

    ⬆ [pre-commit.ci] pre-commit autoupdate
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  2. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)
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Commits on Aug 23, 2023

  1. Merge pull request #111 from florianjoerg/pre-commit-ci-update-config 

    ⬆ [pre-commit.ci] pre-commit autoupdate
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  2. started on idea for acceptor and donor modes for each residue, settin… 

    …g H and D nonbonded parameters extra after transfer
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  3. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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  4. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Aug 25, 2023

  1. started reusing stuff from the h2oac branch for donor/acceptor modes

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  2. tests

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  3. resolved merge conflict

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Commits on Aug 31, 2023

  1. updates mainly to update.py to include donor/acceptor modes

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  2. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Sep 1, 2023

  1. small corrections

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Commits on Sep 4, 2023

  1. ⬆ [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.285...v0.0.287)
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Commits on Sep 5, 2023

  1. mda reader for openmm rst files

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  2. Merge pull request #113 from florianjoerg/mda_xml_reader 

    mda reader for openmm rst files
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  3. Merge branch 'main' into pre-commit-ci-update-config

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  4. Merge pull request #112 from florianjoerg/pre-commit-ci-update-config 

    ⬆ [pre-commit.ci] pre-commit autoupdate
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  5. Update helpers.py

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  6. Update helpers.py

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  7. Update test_helpers.py

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Commits on Sep 6, 2023

  1. Update README.md

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Commits on Sep 7, 2023

  1. first idea to save and load residues and setup donor and acceptor par… 

    …ameters so that we don't have to manipulate the psf
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  2. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Sep 22, 2023

  1. Merge branch 'main' of github.com:florianjoerg/protex into tetr_marta

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Commits on Sep 26, 2023

  1. new force field files for toh2

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  3. started debugging code with test_h2o.py

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  4. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Oct 2, 2023

  1. debugging

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Oct 11, 2023

  1. debugging (ordered names, H_D parms)

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Commits on Oct 17, 2023

  1. debugging

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Oct 18, 2023

  1. CustomNonBondedForce works only with fast

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Oct 20, 2023

  1. changes to donor/acceptor modes, still need to think about when to up… 

    …date them
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Commits on Nov 2, 2023

  1. debugging

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Commits on Nov 14, 2023

  1. saving and loading whole protex system

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Commits on Nov 16, 2023

  1. fixed parameters not being saved and loaded

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Nov 17, 2023

  1. use HBonds per default for water systems, cleanup of notes and todos

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Nov 20, 2023

  1. removed unused pair_13_list

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Dec 4, 2023

  1. fixing bug with DrudeForceThole (not present in water)

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Commits on Dec 6, 2023

  1. larger changes to check is force is present for each residue before t… 

    …rying to update
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Commits on Dec 13, 2023

  1. fixing drude vs drudethole problem

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

    …_marta
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Commits on Dec 14, 2023

  1. fixing detect_forces

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

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  3. 🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks

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Commits on Jan 4, 2024

  1. changed extract_templates to account for residues being bound togethe… 

    …r in proteins
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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

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  1. fixing CustomNonbondedForce, now updating NBF and CNBF for each H and D

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  2. Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr… 

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  1. trying to find a way to update nonbonded exclusions for H/D, needs a … 

    …lot of refining
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  1. working on customnonbondedforce

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  2. Merge branch 'tetr_marta' of github.com:cbc-univie/protex into tetr_m… 

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