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• 3aa91626db Update README for 0.16.0 (#439) main 0.16.0 Evan Pretti 2026-04-27 10:34:40 -07:00
• 745cfcfa80 Make all template generators require explicit force field specification (#438) Evan Pretti 2026-04-24 13:30:35 -07:00
• 5bf74f7655 Update README and SystemGenerator docstring (#435) Evan Pretti 2026-04-24 12:23:32 -07:00
• 4fda9f1388 [pre-commit.ci] pre-commit autoupdate (#436) pre-commit-ci[bot] 2026-04-06 11:20:06 -07:00
• 7b765ec034 Support multi-residue molecules in template generator and improve performance (#430) Evan Pretti 2026-03-31 17:03:58 -07:00
• 0fdae52b7f Bump mamba-org/setup-micromamba from 2 to 3 (#433) dependabot[bot] 2026-03-27 09:24:10 -07:00
• d2575521db Bump codecov/codecov-action from 5 to 6 (#432) dependabot[bot] 2026-03-26 13:15:32 -05:00
• a4cf0cfce9 Bump docker/login-action from 3 to 4 (#431) dependabot[bot] 2026-03-04 09:07:51 -08:00
• 0551fd1fa5 SMIRNOFF: multiple force field files, virtual sites, and constraints (#423) Evan Pretti 2026-03-03 13:49:52 -08:00
• fb8ed0eda4 [pre-commit.ci] pre-commit autoupdate (#427) pre-commit-ci[bot] 2026-01-06 08:58:32 -08:00
• 2df3b57acd Add changelog entry for 0.15.1 (#425) 0.15.1 Mike Henry 2025-12-18 15:01:54 -07:00
• 1c969a638f Bump actions/checkout from 5 to 6 (#420) dependabot[bot] 2025-11-21 11:06:58 -06:00
• cbfa007fb8 Remove ff19ipq (#419) Evan Pretti 2025-11-18 11:10:23 -08:00
• 2b42b442bb Make default SMIRNOFF force field openff-2.2.1 (#417) Evan Pretti 2025-11-13 14:20:22 -08:00
• ea248b423f Bump OpenMM versions in CI to include 8.4.0 (#418) Evan Pretti 2025-11-12 17:07:13 -08:00
• a81f28a0d8 Allow for any barostat in SystemGenerator (#414) Hannah Baumann 2025-11-04 01:50:34 +01:00
• 839f225e00 [pre-commit.ci] pre-commit autoupdate (#407) pre-commit-ci[bot] 2025-10-14 12:58:22 -07:00
• a41df65465 Fix CI, update docstrings (#408) Matt Thompson 2025-10-08 17:25:48 -05:00
• 48a0b54655 Add Lipid21 (#390) Evan Pretti 2025-09-08 14:11:11 -07:00
• 44b7d6709f Using stdlib importlib.resources instead (#403) Iván Pulido 2025-08-21 08:12:47 -04:00
• a9a41bbcef Bump actions/checkout from 4 to 5 (#402) dependabot[bot] 2025-08-11 15:56:14 -05:00
• 6d91c7099e Release 0.15.0 (#401) 0.15.0 Mike Henry 2025-08-07 15:43:07 -07:00
• 0496840ca5 Import DGL to create ~/.dgl/config.json before any tests run (#400) Evan Pretti 2025-08-06 15:52:11 -07:00
• 301dad9e75 Fixes for issues and assorted cleanups to generators (#391) Evan Pretti 2025-08-06 12:38:04 -07:00
• 6f372f04d6 Merge pull request #397 from epretti/remove-dummysystemgenerator Evan Pretti 2025-08-06 10:12:48 -07:00
• 7994d1969e Merge branch 'main' into remove-dummysystemgenerator Mike Henry 2025-08-06 08:25:27 -07:00
• e7c1f9e5e8 Fix espaloma model download race conditions (#398) Evan Pretti 2025-08-06 08:06:38 -07:00
• 4795d124f8 Remove DummySystemGenerator Evan Pretti 2025-08-05 14:02:36 -07:00
• 06edadece1 Merge pull request #392 from openmm/feat/run-espaloma-tests Evan Pretti 2025-08-01 13:54:43 -07:00
• 936291a6e3 put env block up higher in job step so it is easier to see and also fix issue with it missing Mike Henry 2025-07-30 14:27:06 -07:00
• fd86f96ff4 need to also not use --runespaloma on python 3.13 Mike Henry 2025-07-30 14:13:35 -07:00
• c5e773e726 skip espaloma tests on python 3.13 (might need to also remove --runespaloma in pytest call if we are on python 3.13 -- lets see what happens) Mike Henry 2025-07-30 13:17:41 -07:00
• a483303b14 Merge branch 'main' into feat/run-espaloma-tests Mike Henry 2025-07-28 10:29:55 -07:00
• 5d0c60724a drop python 3.10, add 3.13 and drop openmm 8.1.2 and test 8.3.1 (#394) Mike Henry 2025-07-28 10:29:41 -07:00
• 580cd58611 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-07-25 19:09:33 +00:00
• 722c2f61b6 Run espaloma tests and refactor CMMotionRemover fix Mike Henry 2025-07-25 12:06:59 -07:00
• 6c90ebbd60 install espaloma Mike Henry 2025-07-25 11:44:07 -07:00
• b2998133fe Update README to reflect default SMIRNOFF force field (#389) Matt Thompson 2025-07-15 15:39:01 -05:00
• 624b6905e9 [pre-commit.ci] pre-commit autoupdate (#388) pre-commit-ci[bot] 2025-07-07 17:56:02 +00:00
• 4f9228dc7b Merge pull request #386 from epretti/charmm-naming-patching Evan Pretti 2025-07-02 11:17:33 -07:00
• 34c07f042b Drude fixes and better improper/anisotropy script template name lookup Evan Pretti 2025-06-23 17:33:51 -07:00
• 2f8440dfc3 Add Drude version of all-amino-acid test with terminal residues Evan Pretti 2025-06-23 16:27:42 -07:00
• 842adfee6d Allow combining CHARMM force fields with others not using residue+name atom type scheme. Evan Pretti 2025-06-23 14:44:19 -07:00
• b4d5917fee Add tests case with standard amino acids including N- and C-terminals Evan Pretti 2025-06-23 14:21:23 -07:00
• 8412e01819 Update README to note issues with current ParmEd and point to patched repository Evan Pretti 2025-06-23 12:44:20 -07:00
• 2a223fad29 Merge branch 'fix-charmm-proline-patch' into charmm-naming-patching Evan Pretti 2025-06-23 11:13:34 -07:00
• 61c6bd1c31 Don't apply proline-specific patch to non-proline residues Evan Pretti 2025-06-23 11:12:07 -07:00
• 730a101933 Merge pull request #385 from openmm/fix-numpy.compat-issue Evan Pretti 2025-06-23 09:18:50 -07:00
• 74b6557123 Pin numpy <2.3 to fix issue with numpy.compat missing Mike Henry 2025-06-20 12:32:48 -07:00
• 08e4c22dcf Merge pull request #368 from epretti/update-amber-ff Evan Pretti 2025-04-30 14:46:57 -07:00
• 2af04a3289 Skip EP site in prefix for compatibility Evan Pretti 2025-04-30 12:00:00 -07:00
• 3f73b6ff97 Add prefixes to class attributes to avoid any possible collisions Evan Pretti 2025-04-30 11:23:34 -07:00
• 9073e9b7e6 Update README files Evan Pretti 2025-04-30 11:15:23 -07:00
• dca03db053 Add more GLYCAM, lipid, and protein+RNA+DNA testing Evan Pretti 2025-04-29 17:03:48 -07:00
• 97153ee1e2 Regenerate all force field files Evan Pretti 2025-04-17 13:41:00 -07:00
• ba73c88204 Merge branch 'main' into update-amber-ff Evan Pretti 2025-04-17 13:37:40 -07:00
• 1d82469cd5 GLYCAM compatibility with protein force fields for HYP Evan Pretti 2025-04-17 13:36:06 -07:00
• 7f0201b413 set weights_only=False to ensure compatibility with torch>2.6 (#375) Niklas Rindtorff 2025-04-17 21:37:15 +02:00
• 7f0882ac0e Merge branch 'main' into update-amber-ff Evan Pretti 2025-04-16 16:13:20 -07:00
• ae76e9dbc2 Merge pull request #370 from openmm/improve-molecule-filtering Evan Pretti 2025-04-10 12:38:47 -07:00
• 6162834986 Better names for skip marks for espaloma/gaff tests Evan Pretti 2025-04-10 11:16:34 -07:00
• 570e1e434c Merge branch 'main' into improve-molecule-filtering Evan Pretti 2025-04-10 11:12:14 -07:00
• 37bec91b4c [pre-commit.ci] pre-commit autoupdate (#374) pre-commit-ci[bot] 2025-04-08 13:55:50 -05:00
• 47c601b1fa Filter to smaller molecules for CI since sqm is extremely slow Evan Pretti 2025-04-01 13:49:28 -07:00
• fc9ae6facb [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] 2025-04-01 16:47:53 +00:00
• 87c20aabed test_charge_from_molecules uses partial charges that sum to expected total Evan Pretti 2025-04-01 09:47:16 -07:00
• 0f838105d4 Merge remote-tracking branch 'upstream/main' into improve-molecule-filtering Evan Pretti 2025-04-01 09:05:31 -07:00
• 8b77a41812 GAFF test flag mark is called gaff, not rungaff Evan Pretti 2025-04-01 09:04:23 -07:00
• bb5f7992c7 Fix test_jacs_complexes Evan Pretti 2025-04-01 09:03:33 -07:00
• 78550eb295 Make filter_molecules work for parmed structures as well Matthew W. Thompson 2025-03-28 13:37:10 -05:00
• fc94b5493c Minimize conformer before running dynamics Matthew W. Thompson 2025-03-24 14:57:11 -05:00
• 0d507dfcbe Improve error reporting Matthew W. Thompson 2025-03-24 10:31:57 -05:00
• 60d77420df Actually skip when force field filtered Matthew W. Thompson 2025-03-24 10:10:52 -05:00
• e034996e39 Lint Matthew W. Thompson 2025-03-22 10:20:31 -05:00
• 882632f0b4 Refactor filtering OpenFF force fields Matthew W. Thompson 2025-03-22 10:13:43 -05:00
• eaa1c4ac19 Small testing improvements Matthew W. Thompson 2025-03-21 13:45:21 -05:00
• a011a03f16 Also skip SPC/E Matthew W. Thompson 2025-03-21 12:53:55 -05:00
• f55cd08c1b Skip Sage candidate with bad angle parameter(s) Matthew W. Thompson 2025-03-21 10:04:33 -05:00
• d905122064 Fix Matthew W. Thompson 2025-03-21 09:22:52 -05:00
• d4dc780ca4 Improve molecule filtering in tests Matthew W. Thompson 2025-03-21 09:08:50 -05:00
• 675f14ad6d Update CHARMM force field to July 2024 release (#356) Evan Pretti 2025-03-26 16:46:53 -07:00
• d5022d733a Merge pull request #371 from epretti/fix-multiple-registration Evan Pretti 2025-03-24 09:17:28 -07:00
• f1810217b1 Don't turn on the GAFF tests yet in this PR, but make necessary changes Evan Pretti 2025-03-21 13:21:52 -07:00
• 62c6f0eedd Remove duplicate atom type handling and re-enable GAFF tests Evan Pretti 2025-03-21 09:56:12 -07:00
• caf24fefda Shorten line length in docstring Evan Pretti 2025-03-20 17:39:37 -07:00
• 0868c5bc07 Re-enable some GAFF tests (except the ones failing due to #369) Evan Pretti 2025-03-20 15:33:12 -07:00
• 53b4a12cce Update system generator tests for GAFF 2.2.20 Evan Pretti 2025-03-20 15:33:00 -07:00
• b820a5f0bb Update generators for GAFF 2.2.20 Evan Pretti 2025-03-20 15:32:21 -07:00
• ca17fb9d23 Update README file Evan Pretti 2025-03-20 15:25:54 -07:00
• 292c38249c Fix failing test for CI Evan Pretti 2025-03-20 10:50:35 -07:00
• 98a6fe899b Added entries for phosphorylated FFXML dependencies to test Evan Pretti 2025-03-14 14:32:46 -07:00
• cce122c6b7 Hopefully final regeneration of FFXML files Evan Pretti 2025-03-14 13:33:57 -07:00
• 5bdcbf93c8 GLYCAM now fixed using new algorithm to find external bonds in ParmEd Evan Pretti 2025-03-14 12:18:07 -07:00
• 016e67b880 Put back old GLYCAM since automated conversion is broken Evan Pretti 2025-03-13 16:31:55 -07:00
• 88df0b65a6 Fix GLYCAM script formatting Evan Pretti 2025-03-13 14:10:39 -07:00
• 3ed304cc99 Revert incorrectly updated version numbers Evan Pretti 2025-03-13 13:43:55 -07:00
• 90d1de29ad Update README and remove outdated test files Evan Pretti 2025-03-13 13:01:12 -07:00
• 20a4e222ed Merge branch 'main' into update-amber-ff Evan Pretti 2025-03-13 12:39:02 -07:00
• f57e3856f3 Fix #357 Evan Pretti 2025-03-13 12:36:16 -07:00
• b6004b32e2 Update package version numbers Evan Pretti 2025-03-13 12:17:08 -07:00