Release 2026.2.0 - #208

Merged

lohedges merged 85 commits into

mainfrom

release_2026.2.0

Sep 15, 2026

Commits on Jun 29, 2026

Update BioSimSpace development pin.
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f58b8f1
Update CHANGELOG for 2026.2.0 development.
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ebcc92c
Add note regarding PyMBAR JAX issues.
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e5c79f4

Commits on Jul 1, 2026

Remove pre-release warning. [ci skip]
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c2f5660
Clarify perturbed_system option. [ci skip]
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5eb74ec

Commits on Jul 2, 2026

Add support for generating Boresch restraints for ABFE.
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65ccd41
Add support for split restraint levers in ABFE schedules.
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2c572de

Commits on Jul 3, 2026

Commits on Jul 4, 2026

Seed simulation from least strained restraint search structure.
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196237b

Commits on Jul 21, 2026

Commits on Jul 22, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Store GCMC statistics per lambda value.
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688ac1f
Merge pull request #185 from OpenBioSim/feature_gcmc_stats
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54ffab8
Use pip_check: false to avoid NumPy pin errors with AmberTools.
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6b21af9

Commits on Aug 4, 2026

Link restart systems to the reference end state.
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696344f
Merge pull request #189 from OpenBioSim/fix_188
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774bcf1
Cap the number of OpenMM contexts used for replica exchange.
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d4e98bd
Fix constrained bond lengths at a common lambda value.
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602b502
Seed the end state from the middle of a group.
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7aa1d55
Check that replicas resume from where they stopped.
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dbf257c
Read positions from a legacy checkpoint when logging the GCMC sphere.
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da97daf
Set the box vectors before the positions.
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dd98085
Accumulate the flags for replicas whose state has moved.
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78c8d68
Don't minimise on restart.
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4b19dfd
Consolidate the duplicated context count and GPU load warnings.
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b05c162
Document max_contexts in the replica exchange section of the README.
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9359110
Fix typos and formatting errors in README.
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e297c24
Pin the perturbed system coordinate path in the seeding test.
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9e97ff1
Respect swap_end_states when seeding from the perturbed system.
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06534ff
Clarify what the perturbed_system input must contain.
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6596422
Suggest a max_contexts value when the replicas don't fit in memory.
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3a95b4b
Remove the redundant post-equilibration GCMC water count.
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d28a6df
Assert that GCMC water occupancy follows the replica through a mix.
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0c2e302
Count the GCMC waters against the context in the regular runner.
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23d29fa
Cover GCMC with no sampling region in the regular runner.
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b1d0e6f
Pre-equilibrate the water before minimising in the regular runner.
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682e5c9
Give each replica its own terminal flip statistics list.
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6a80168
Link CHANGELOG entries to PR.
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c51911d
Add a precision option for GPU platforms.
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ac9b1e6

Commits on Aug 5, 2026

Commits on Aug 24, 2026

Add section on keeping up-to-date during a development cycle. [ci skip]
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fdec2e7
Add support for auto-generating Morse restraints for ring-breaking.
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771c8cd
Document schedules, ABFE, and ring-breaking. [ci skip]
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57f3693
Merge pull request #194 from OpenBioSim/feature_auto_rb_restraint
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f689ad3
Document intended use of standard_morph schedule. [ci skip]
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666898e
Remove redundant prepareFEP option. [ci skip]
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c681d7f
Make package name formatting consistent. [ci skip]
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0ebf66f
Correct version scheme. [ci skip]
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7289440

Commits on Aug 26, 2026

Commits on Aug 28, 2026

Don't silently swallow errors when adding coalchemical restraints.
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e8c1b13
Add section on charge-change perturbations. [ci skip]
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95eb838
Add features section to the top of the README. [ci skip]
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97092ac
Add link to somd2_examples repository. [ci skip]
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d1bc0d6
Accept stream file paths for restraints and lambda schedules.
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3384ca7
Merge pull request #198 from OpenBioSim/feature_stream_file_input
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9b7651b
Fix log message.
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9217a47

Commits on Sep 1, 2026

Fix platform section. [ci skip]
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b462843

Commits on Sep 4, 2026

Account for v-site charges when checking for charge change.
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b46b16b
Merge pull request #200 from OpenBioSim/fix_199
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2aaee8c

Commits on Sep 8, 2026

Handle num_lambda=1.
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4734d57
Update CHANGELOG and add missing entries and links.
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05e447b
Merge pull request #203 from OpenBioSim/fix_202
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2662187

Commits on Sep 14, 2026

Default to single precision until benchmarks are done.
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08f7b8d

Commits on Sep 15, 2026

Use the configured platform when detecting available GPUs.
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2e4d519
Fix the OpenCL constant used to query AMD GPU free memory.
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e25aa48
Merge pull request #206 from OpenBioSim/fix_204_205
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a201bc7
Merge branch 'main' into release_2026.2.0
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c4d831d
Update BioSimSpace pin.
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ca848fc
Update CHANGELOG.
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b60f2ab