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Mono Color

• 3adb413691 Merge branch 'master' into toolkit-update Mike Henry 2022-07-12 13:53:55 -07:00
• 1bdba6b112 Fix missing import John Chodera 2022-07-12 12:48:01 -04:00
• 319ca47d4d Add TODO to use hash in future John Chodera 2022-07-12 09:45:37 -04:00
• eb0f0d0970 Fix #211 : Use basename instead of filepath for cache generation John Chodera 2022-07-12 09:44:34 -04:00
• f9b08ea218 Merge pull request #212 from openmm/fix-gaff2 John Chodera 2022-07-12 06:41:21 -07:00
• 051b2427c4 Fix logic in detecting gaff version John Chodera 2022-07-12 09:05:36 -04:00
• c1b07861d3 Fix #210: gaff atom type name is now correctly passed John Chodera 2022-07-12 01:38:58 -04:00
• 815dfd1d52 Merge pull request #208 from openmm/fix-tests John Chodera 2022-07-11 22:26:07 -07:00
• b8cd9a0175 Test against espaloma master to see if bugfix addresses test failure John Chodera 2022-07-12 00:44:31 -04:00
• 975773c4e2 Remove voluminous debug output John Chodera 2022-07-10 18:22:10 -04:00
• 95afb47eca Reduce number of molecules for CI tests John Chodera 2022-07-10 17:48:11 -04:00
• 583be46deb Fix critical bug introduced in PR #198 that meant no torsions were converted into templates John Chodera 2022-07-10 16:49:25 -04:00
• 29e186f0f2 Fix and generalize tests to produce more useful error message John Chodera 2022-07-10 16:30:00 -04:00
• 08afe1681e Fix bug in refactored code John Chodera 2022-07-10 12:12:33 -07:00
• ddd4503afc More debug information John Chodera 2022-07-09 21:33:49 -07:00
• 8cb79796e4 Refactor to eliminate some duplication and add debug XML output John Chodera 2022-07-09 21:06:30 -07:00
• 7095e66355 Change how we measure relative deviation in vectors to avoid underflow. John Chodera 2022-07-09 19:59:44 -07:00
• 7e2c769003 remove leftover bit from debugging Mike Henry 2022-05-16 15:30:03 -07:00
• 99224ac3fc Bump codecov/codecov-action from 2.1.0 to 3.1.0 dependabot[bot] 2022-05-16 17:51:29 +00:00
• e5fd0dde2f Fix CI (#202) Mike Henry 2022-05-16 10:50:05 -07:00
• f3e93f1161 Remove debug prints. (#198) Iván Pulido 2022-05-16 13:49:26 -04:00
• 53c62cc0d5 Remove espaloma debug line (#201) Mike Henry 2022-05-16 10:49:05 -07:00
• c5dc34c8a1 Bump actions/checkout from 2 to 3.0.2 dependabot[bot] 2022-04-21 15:08:25 +00:00
• ccd6b9daa5 Merge pull request #195 from openmm/espaloma-readme 0.11.0 John Chodera 2022-04-10 18:09:00 -07:00
• f0c3b1e49f Fix references to espaloma-0.2.2 in README John Chodera 2022-04-10 18:08:03 -07:00
• 1fabf4359a Merge pull request #182 from openmm/espaloma John Chodera 2022-04-07 11:30:13 -07:00
• 5b219a4162 Fix detection of whether tests are running on CI John Chodera 2022-04-07 08:20:09 -07:00
• 9816f01d16 Update SystemGenerator tests to use espaloma-0.2.2 John Chodera 2022-04-07 08:09:11 -07:00
• f8d989001f Fix retrieve forcefield test John Chodera 2022-04-06 20:29:07 -07:00
• 2af3603a01 We're using espaloma-x.y.z.pt for naming models now, not espaloma_x.y.z.pt John Chodera 2022-04-06 16:23:26 -07:00
• f4fe71a1bc Test on Python 3.7, 3.8, 3.9 John Chodera 2022-04-05 21:24:26 -07:00
• 8263899fd8 Fix typo in test calls to ForceField.createSystem() John Chodera 2022-04-05 21:04:52 -07:00
• 617c5d9315 Update to espaloma-0.2.2 John Chodera 2022-04-05 20:32:42 -07:00
• bbddefb278 Merge remote-tracking branch 'upstream/master' into toolkit-update Matthew W. Thompson 2022-03-28 11:26:47 -05:00
• 2195abab82 Update SMIRNOFFTemplateGenerator for toolkit API breaks Matthew W. Thompson 2022-03-28 11:25:52 -05:00
• d7b1b2eabc Remove debug code John Chodera 2022-03-03 20:53:23 -08:00
• 4b4c3e08b6 Handle espaloma with SMIRNOFF torsions. John Chodera 2022-03-03 20:51:21 -08:00
• 99a4b43553 Debugging espaloma John Chodera 2022-03-02 06:44:55 -08:00
• 1dab2f1151 Ensure we use a sufficiently recent qcportal John Chodera 2021-12-20 17:41:20 -08:00
• b3abca381f Update INSTALLED_FORCEFIELDS John Chodera 2021-11-14 22:57:56 +01:00
• 23dc2af72c Fix error in EspalomaTemplateGenerator.INSTALLED_FORCEFIELDS John Chodera 2021-11-14 20:29:39 +01:00
• a965bea403 Log charge discrepancies as INFO John Chodera 2021-11-14 17:57:36 +01:00
• 54d1f95d62 Update espaloma charge generation to use new API to allow charging from nn or molecule John Chodera 2021-11-14 16:36:09 +01:00
• 94d86fa77c Update conda env to test against espaloma master John Chodera 2021-11-14 16:32:45 +01:00
• 036762b0a9 Merge remote-tracking branch 'origin/master' into espaloma John Chodera 2021-11-14 16:31:37 +01:00
• ddea4f61d5 Bump codecov/codecov-action from 2.0.3 to 2.1.0 (#179) dependabot[bot] 2021-11-11 02:39:13 +00:00
• 3783cc8acf Fix glycam ffxml and conversion script (#180) zhang-ivy 2021-11-10 18:47:43 -05:00
• d06c944284 Add qcportal to conda env requirements, since espaloma seems to require it? John Chodera 2021-10-28 23:27:15 -07:00
• 0b9803daaa Update README with espaloma use instructions John Chodera 2021-10-28 22:33:04 -07:00
• f7d0142381 Fix indentation in test environment YAML John Chodera 2021-10-28 22:18:42 -07:00
• 3268267c62 Add espaloma to SystemGenerator tests John Chodera 2021-10-28 22:16:51 -07:00
• 5597b73150 Fix test env YAML John Chodera 2021-10-28 22:16:40 -07:00
• 243709b15f Initial implementation of EspalomaTemplateGenerator and unit tests John Chodera 2021-10-28 22:11:59 -07:00
• e027de0941 Refactor OpenMM System -> ffxml conversion into mixin John Chodera 2021-10-28 18:45:27 -07:00
• 73a0707dc6 Merge pull request #173 from openmm/fix-tests-for-openmm-7.6 0.10.0 John Chodera 2021-09-08 16:33:25 -07:00
• 56df8e35c7 Merge remote-tracking branch 'origin/master' into fix-tests-for-openmm-7.6 John Chodera 2021-09-08 10:43:03 -07:00
• 65ab4345e0 Merge pull request #177 from openmm/fix-test-glycam John Chodera 2021-09-08 10:42:09 -07:00
• 4ce38691ab fix resource_filename Ivy Zhang 2021-09-08 09:42:34 -04:00
• 21b00cc768 use protein.ff14SB not ff14SB Ivy Zhang 2021-09-08 09:32:37 -04:00
• 2d83fd879b include ff14SB when testing glycam Ivy Zhang 2021-09-08 09:22:17 -04:00
• 599f0638a6 Merge remote-tracking branch 'origin/master' into fix-tests-for-openmm-7.6 John Chodera 2021-09-04 13:53:42 -07:00
• 65fb59eb27 Merge pull request #156 from zhang-ivy/convert-glycans John Chodera 2021-09-01 14:24:48 -07:00
• 6f4b7be765 Merge remote-tracking branch 'origin/master' into fix-tests-for-openmm-7.6 John Chodera 2021-08-31 20:13:33 -07:00
• 0f0d014377 Merge branch 'master' into convert-glycans Mike Henry 2021-08-31 14:27:33 -07:00
• 6ac4ea5969 Don't interpret regex match strings as escape characters. John Chodera 2021-08-27 18:01:02 -07:00
• 401c271b68 Merge pull request #171 from openmm/dependabot/github_actions/codecov/codecov-action-2.0.3 John Chodera 2021-08-27 17:54:10 -07:00
• d2faa82e6c Update README changelog John Chodera 2021-08-27 17:51:56 -07:00
• 534bd4ee34 Update all simtk.openmm -> openmm and simtk.unit -> openmm.unit imports for OpenMM 7.6; pin to >=7.6 John Chodera 2021-08-27 17:48:27 -07:00
• 6956b5c8a7 Merge branch 'master' into dependabot/github_actions/codecov/codecov-action-2.0.3 Mike Henry 2021-08-26 17:32:56 -07:00
• 5fee63ab13 Merge pull request #167 from openmm/fix/dependabot Mike Henry 2021-08-26 14:36:22 -07:00
• bbb23a977d Merge branch 'master' into fix/dependabot Mike Henry 2021-08-26 11:31:23 -07:00
• f9d46b524c Bump codecov/codecov-action from 1 to 2.0.3 dependabot[bot] 2021-08-25 15:09:29 +00:00
• de8aab5ef4 switch test case to be glyco proteins john sent Ivy Zhang 2021-08-09 15:30:16 -04:00
• 663ba4a1dd fix dependabot so it can see our secrets Mike Henry 2021-07-21 09:19:23 -07:00
• 352fcebb4c add global flag controlling external bond code in parmed and change files/glycan -> files/glycam name Ivy Zhang 2021-07-13 16:17:24 -04:00
• ba00644c8e remove _modified from ffxml name Ivy Zhang 2021-07-13 13:55:04 -04:00
• 788b6e44ba clean up convert_amber.py and update helper files Ivy Zhang 2021-07-13 13:42:29 -04:00
• b73b6b0e42 remove accidentally change Ivy Zhang 2021-03-30 12:01:25 -04:00
• be75ca7cf9 simplify assert energies Ivy Zhang 2021-03-30 11:59:10 -04:00
• 4b0a7b3710 add files used for ff conversion and changes needed to run validation test Ivy Zhang 2021-03-05 17:17:06 -05:00
• 44109f20f3 add ffxml Ivy Zhang 2021-03-04 20:47:55 -05:00
• b3416c3b3d add override to yaml and initial test for glycoprotein Ivy Zhang 2021-02-26 23:51:37 -05:00
• ca9319f15d Testing CI (#155) Mike Henry 2021-02-06 18:08:39 -07:00
• 991216c9cf Merge pull request #153 from openmm/update-readme 0.9.0 John Chodera 2021-02-05 12:09:47 -08:00
• 98f88e6f3e Fix incorrect topology object documentation in README John Chodera 2021-02-05 09:58:10 -08:00
• 32cf7876cf Update README for conda-forge John Chodera 2021-02-05 09:55:19 -08:00
• a2b8bf7c7d Merge pull request #151 from openmm/update-readme John Chodera 2021-02-05 09:47:23 -08:00
• 3fb0cc3c15 More typos John Chodera 2021-02-04 23:16:25 -05:00
• a9f20290b4 Fix typo John Chodera 2021-02-04 23:06:30 -05:00
• 5592e0ed72 Fix amber unit test John Chodera 2021-02-04 22:48:38 -05:00
• 739c1bc5ad Update CHARMM to July 2020 release; delete toppar so parameters are retrieved before conversion John Chodera 2021-02-04 20:05:26 -05:00
• d5628bd3dc Update READMEs John Chodera 2021-02-04 20:00:16 -05:00
• fe144eaba0 Update all Amber force fields to AmberTools 20.15 John Chodera 2021-01-26 16:31:47 -05:00
• 449ce52b5e Update phosphorylation test files John Chodera 2021-01-26 13:14:48 -08:00
• d78239315c Update README for AMBER conversion John Chodera 2021-01-26 13:10:18 -08:00
• 771c2658ff Add glycan test PDB John Chodera 2021-01-26 12:58:40 -08:00
• 06da10ca80 Update for AmberTools 20.14 John Chodera 2021-01-26 12:45:54 -08:00
• dbec7cc1c4 Merge pull request #149 from openmm/gha-update John Chodera 2021-01-26 11:20:28 -08:00
• b29ace757c Skip CHARMM conversion tests until new ParmEd is released John Chodera 2021-01-26 07:48:55 -08:00
• c4d9ab77d1 Update build status badge for master branch John Chodera 2021-01-23 12:59:55 -08:00