Commit Graph

  • 5ae1e72a65 deep copy bonds (#5307) master Vyom Patel 2026-06-02 13:48:45 -04:00
  • 335e6865f3 Fix AmoebaMultipoleForce::ForceInfo particle groups used for molecule detection and atom reordering (#5302) cmd23333 2026-06-02 02:49:16 +08:00
  • 06d8d51329 Amortize PME atom-grid re-sort for large systems (#5305) Mateus R 2026-05-29 20:52:44 -04:00
  • 2ffa7cd36e Minor cleanup to PythonForce (#5304) Peter Eastman 2026-05-29 17:49:33 -07:00
  • 35d4ce904f Handle hipErrorFileNotFound gracefully in ROCm 7 (#5303) Tom Benson 2026-05-29 13:43:07 -04:00
  • 36a30cbca5 Changes for 8.5.2 (#5297) 8.5_branch Peter Eastman 2026-05-28 11:12:52 -07:00
  • fc21fd1923 Compile correctly under newer C++ standards (#5296) Peter Eastman 2026-05-27 11:01:05 -07:00
  • c6f9fab280 More barostats support scaling particles independently (#5278) Peter Eastman 2026-05-26 07:37:26 -07:00
  • f99249f5c3 docs: document atom-to-particle index correspondence (#5289) Sai Asish Y 2026-05-19 08:55:10 -07:00
  • 58749d9d84 Try to get docs build working (#5282) Peter Eastman 2026-05-07 18:02:55 -07:00
  • aa8ec1a8e9 SimulatedTempering uses ExpandedEnsembleSampler (#5281) Peter Eastman 2026-05-07 11:30:27 -07:00
  • ce9fcace1c Created ExpandedEnsembleSampler (#5265) Peter Eastman 2026-05-05 12:18:10 -07:00
  • 14f8b06118 Make sure contexts are deselected before evaluation (#5279) Evan Pretti 2026-05-04 16:26:18 -07:00
  • 0aee805025 Avoid host wait for PME post-computation synchronization (#5271) one 2026-04-30 03:25:58 +08:00
  • 46376ea3e4 Created ReplicaExchangeReporter (#5261) Peter Eastman 2026-04-17 15:29:39 -07:00
  • efd891695c Created ReplicaExchangeSampler (#5257) Peter Eastman 2026-04-10 07:58:58 -07:00
  • 64254c09da Retry error when checking for broken links (#5258) Peter Eastman 2026-04-07 08:31:12 -07:00
  • 9aae4bb35c PythonForce can be restricted to a subset of particles (#5246) Peter Eastman 2026-04-06 14:11:45 -07:00
  • 6717a85cc4 Reduced memory used by SerializationNode (#5249) Peter Eastman 2026-04-06 14:10:16 -07:00
  • f7fa0c27c1 Update version number to 8.5.1 (#5254) 8.5.1 Peter Eastman 2026-04-03 09:13:17 -07:00
  • 337418fd00 Merge fixes for 8.5.1 (#5253) Peter Eastman 2026-04-02 17:10:14 -07:00
  • 1f2203f60b Fixed pressure calculation in MOnteCarloFlexibleBarostat (#5251) Peter Eastman 2026-04-02 15:03:25 -07:00
  • 9f17d0f884 Infrastructure for multistate sampling (#5231) Peter Eastman 2026-04-02 10:45:18 -07:00
  • e4728a2160 atomFlags switched to unordered_map for performance (#5247) ramdoys 2026-03-31 19:46:07 -04:00
  • 5d8d5874b9 Avoid multiple forces running on the worker thread at once (#5243) Peter Eastman 2026-03-30 08:17:46 -07:00
  • 1c528ca842 Take line search energy difference on CPU before reducing precision (#5242) Evan Pretti 2026-03-27 09:08:24 -07:00
  • 26df7a8725 Cache coefficients for long range correction (#5239) Peter Eastman 2026-03-27 08:54:42 -07:00
  • 13c568d08d Fix leaked variable causing spurious template constraint assignment (#5236) Jeff Wagner 2026-03-26 08:49:35 -07:00
  • b55e60882d Update installation instructions (#5227) 8.5.0 Peter Eastman 2026-03-12 10:38:09 -07:00
  • 068495f370 Fix for compilation error on some AMD GPUs (#5224) Peter Eastman 2026-03-04 22:00:41 -08:00
  • 3e8a62ba3f Fixed bug in selecting HIS variant (#5221) Peter Eastman 2026-02-26 14:46:55 -08:00
  • a157923823 Improved documentation on CMMotionRemover (#5219) Peter Eastman 2026-02-24 09:14:45 -08:00
  • 2c287f10fa Fixed issue that caused inefficient sorting when a block contained only one atom (#5215) Peter Eastman 2026-02-19 09:00:55 -08:00
  • acf36fd6e3 Added two more synonyms for HOH (#5213) Peter Eastman 2026-02-17 15:23:16 -08:00
  • bc6fe72928 Update patch documentation (#5208) Yulian Manchev 2026-02-16 18:36:16 +00:00
  • 10b23bf067 Specify extras_require on all platforms (#5207) Peter Eastman 2026-02-11 07:29:28 -08:00
  • 017fca836b Update version number to 8.5 (#5210) Peter Eastman 2026-02-10 13:46:11 -08:00
  • 122dbde222 Avoid error in updateParametersInContext() when there are no exceptions (#5209) Peter Eastman 2026-02-10 12:42:22 -08:00
  • 4ab645ea69 GPU implementation of L-BFGS (#5198) Evan Pretti 2026-02-10 09:22:10 -08:00
  • 834b1294a9 Residue templates can specify constraints (#5197) Peter Eastman 2026-02-09 13:29:40 -08:00
  • add95438df API for querying devices (#5192) Peter Eastman 2026-02-09 11:00:29 -08:00
  • 8eeee16de9 Templates can match whole molecules (#5181) Peter Eastman 2026-01-30 11:16:39 -08:00
  • 421eb42a69 Fix memory error in PythonForce (#5182) Peter Eastman 2026-01-13 17:54:12 -08:00
  • e688b86e20 Fix error reading CONECT records in PDB with multiple models (#5179) Peter Eastman 2026-01-07 16:09:35 -08:00
  • 82703dff73 Fix typos discovered by codespell in Python files (#5173) Christian Clauss 2025-12-30 21:21:00 +01:00
  • 07b738c560 Support ROCm 7 (#5162) Anton Gorenko 2025-12-14 22:33:30 +05:00
  • bb5552c01c Fix uninitialized buffers in QTB (#5163) Anton Gorenko 2025-12-14 03:21:41 +05:00
  • 762d822e14 Prevent running out of disk space in OpenCL CI build (#5164) Peter Eastman 2025-12-13 12:40:50 -08:00
  • adfd84c273 Add LCPO method (#5130) Evan Pretti 2025-12-11 13:28:36 -08:00
  • ccb83f1db9 GromacsTopFile supports vsite type 3fad (#5155) Peter Eastman 2025-12-02 09:51:33 -08:00
  • b0c2c4d84e Minor optimization to PME (#5151) Peter Eastman 2025-12-01 15:53:38 -08:00
  • a112fbfcc7 PDBx/mmCIF files are case insensitive (#5149) Peter Eastman 2025-11-26 09:49:34 -08:00
  • 321934222e Add pythonforce.i to SWIG input files (#5148) 9527567 2025-11-26 02:55:16 +08:00
  • 103b64b3c2 Remove ff19ipq (#5143) Evan Pretti 2025-11-18 12:33:55 -08:00
  • 98173c6041 Workaround for Intel CPU OpenCL 2025.3 (#5137) Evan Pretti 2025-11-13 08:48:12 -08:00
  • 2fbed59258 Created PythonForce (#5122) Peter Eastman 2025-11-12 09:14:19 -08:00
  • 74912095a9 Refactor reference PME (#5131) Peter Eastman 2025-11-11 15:31:38 -08:00
  • c24c619e4f Code cleanup (#5127) Peter Eastman 2025-11-06 12:04:52 -08:00
  • b1a5324c88 Use native ARM Linux runner (#5123) Peter Eastman 2025-11-03 10:01:57 -08:00
  • 47684368db Fixed SymmetrySite on HIP platform (#5118) 8.4.0 Peter Eastman 2025-10-22 12:14:01 -07:00
  • 895fcd4ce8 Avoid incorrectly adding plasma correction (#5117) Peter Eastman 2025-10-22 12:13:49 -07:00
  • 58378cceac Fixed errors in computeCurrentPressure() (#5114) Peter Eastman 2025-10-21 18:19:33 -07:00
  • b64a82a89a Fix issue with constant potential and large neighbor lists (#5109) Evan Pretti 2025-10-21 14:40:57 -07:00
  • 2b20ffbabc Document installing HIP 7 package (#5107) Peter Eastman 2025-10-16 15:42:17 -07:00
  • c19e1d5ab9 Update runner used for Intel Mac CI (#5106) Peter Eastman 2025-10-16 14:16:36 -07:00
  • eaf56f96bc Update AMOEBA XML, .prm files, and parsing of Tinker files (#5086) João Morado 2025-10-14 20:55:21 +01:00
  • 85e0efb6f4 Documentation updates for 8.4 (#5101) Peter Eastman 2025-10-14 11:35:00 -07:00
  • 489e2c46a2 Cleanup TinkerReader, ForceField, and amoebaforces (#5080) João Morado 2025-10-14 16:59:01 +01:00
  • 064cee2fb0 Fix compilation error on CUDA 13 (#5092) Peter Eastman 2025-09-25 09:04:52 -07:00
  • 3076825e19 Update logo, styles and font in documentation (#5090) Evan Pretti 2025-09-25 08:59:23 -07:00
  • 1a67542eef Make distinct parameter dictionaries for _TemplateAtomData by default (#5091) Evan Pretti 2025-09-24 16:22:43 -07:00
  • 05472c9a81 Update file headers (#5074) Evan Pretti 2025-09-23 10:27:26 -07:00
  • 5b07f0d1e8 Install benchmarks and extras (#5085) Peter Eastman 2025-09-19 13:36:09 -07:00
  • ed59d6bc4f Update version number to 8.4 (#5083) Peter Eastman 2025-09-19 10:30:53 -07:00
  • 939e0af545 Reader of Tinker files (#4769) João Morado 2025-09-19 02:00:59 +01:00
  • 227bd68348 Bug fix to QTBIntegrator (#5077) Peter Eastman 2025-09-17 13:04:04 -07:00
  • 0a5be952ce Update constant potential entry in user guide (#5073) Evan Pretti 2025-09-17 09:48:12 -07:00
  • 16efb71b6e Add Lipid21 and update documentation (#5066) Evan Pretti 2025-09-16 09:47:27 -07:00
  • 4507205cf2 Bugfix: Zero-initialize padded posq buffer in AmoebaCommonKernels (#5071) cmd23333 2025-09-13 23:49:44 +08:00
  • f55abcaa5f Add constant potential method (#4870) Evan Pretti 2025-09-12 13:55:50 -07:00
  • 0ad623417f Fix error message formatting related to bonds to extra sites (#5065) Evan Pretti 2025-09-08 09:12:47 -07:00
  • bb3f4f82a8 Fixed bug in calculating plasma self energy correction with offsets (#5069) Peter Eastman 2025-09-06 14:47:09 -07:00
  • d8798cb3db Updated documentation on adding solvent (#5060) Peter Eastman 2025-09-02 13:04:44 -07:00
  • bc05f1c065 merge setDisplacements kernel into copyState (#5058) Emilio Gallicchio 2025-09-02 00:24:43 -04:00
  • c91894e8d4 Bug fix to QTB (#5057) Peter Eastman 2025-08-29 17:33:58 -07:00
  • b4507392ff Drude integrators can find DrudeForce inside another force (#5054) Peter Eastman 2025-08-29 09:11:58 -07:00
  • 54fa65ed0d Created OrientationRestraintForce (#5048) Peter Eastman 2025-08-26 11:44:32 -07:00
  • 44524bd1e7 NBFIX in Gromacs for 1-4 pairs (#5050) feiglab 2025-08-21 20:24:25 -04:00
  • 1b6236a8cc Radius of gyration force (#5031) Peter Eastman 2025-08-14 08:26:25 -07:00
  • 6e2f213fa7 Replace C++ code examples in Python API docs (#5043) Peter Eastman 2025-08-13 15:02:25 -07:00
  • 4958ba269b Forbid LJPME when LJ uses CustomNonbondedForce (#5044) Evan Pretti 2025-08-13 11:55:06 -07:00
  • 3645e1eeb7 Variable distance-based displacements for ATMForce (#4776) Emilio Gallicchio 2025-08-12 15:22:58 -04:00
  • 4a956a72fa Convert C++ types to Python types in API docs (#5036) Peter Eastman 2025-08-12 12:09:57 -07:00
  • 2af004b652 Adaptive quantum thermal bath (#4995) Peter Eastman 2025-08-11 08:03:06 -07:00
  • d2a5d7e409 fix for scaled 1-4 LJ interactions when NBFIX is present in Gromacs topology file (#5032) feiglab 2025-08-07 14:18:11 -04:00
  • 0a4edb841b Fix reading of Gromacs topologies created from CHARMM force field (#5026) feiglab 2025-08-06 19:43:49 -04:00
  • fdea63e9ad Reducing sorting overhead for small systems with PME (#5027) Peter Eastman 2025-08-06 09:03:41 -07:00
  • d2f76949b3 Merge pull request #5030 from epretti/cleanup-examples Evan Pretti 2025-08-05 17:03:07 -07:00
  • 6dfb653015 Fix and update example readme, add openmm.org/development to URL check excludes Evan Pretti 2025-08-05 14:47:06 -07:00
  • 3bbd3bb990 License and links update Evan Pretti 2025-08-05 11:55:16 -07:00