GCMC error

[velocirraptor23]

Hi,

I have installed the developer's version and I have run into some issues with GCMC. When I am not using it, it runs normally.

2026-08-07 10:32:43.607 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.00000
2026-08-07 10:32:43.608 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.10000
2026-08-07 10:32:43.610 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.20000
2026-08-07 10:32:43.612 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.30000
2026-08-07 10:32:43.618 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.40000
2026-08-07 10:32:43.644 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.50000
2026-08-07 10:32:43.659 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.60000
2026-08-07 10:32:43.664 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.70000
2026-08-07 10:32:43.678 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.00000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.679 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.80000
2026-08-07 10:32:43.680 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 0.90000
2026-08-07 10:32:43.681 | INFO | somd2.runner._repex:_minimise:2391 - Minimising at λ = 1.00000
2026-08-07 10:32:43.691 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.10000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.716 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.20000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.718 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.30000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.719 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.40000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.719 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.50000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.720 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.60000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.720 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.70000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.720 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.80000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.721 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 0.90000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.721 | WARNING | somd2.runner._repex:run:1817 - Minimisation failed for λ = 1.00000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:32:43.723 | INFO | somd2.runner._repex:run:1938 - Running dynamics for cycle 1 of 2000
2026-08-07 10:32:43.724 | INFO | somd2.runner._repex:run:1947 - States: [ 0 1 2 3 4 5 6 7 8 9 10]
2026-08-07 10:32:43.815 | ERROR | somd2.runner._repex:run:2004 - Dynamics failed for λ = 0.00000: 'GCMCSampler' object has no attribute 'set_lambda'
2026-08-07 10:45:02.630 | INFO | somd2.runner._base:init:105 - somd2 version: 2026.2.0.dev+52.g8504cc5

somd2 version: 2026.2.0.dev+52.g8504cc5
Many thanks,

Cesar

[lohedges]

This is because you need the development version of the entire stack, including loch, which performs the GCMC sampling.

[velocirraptor23]

Yes, I have checked, and Loch was not updated. I'm doing it now, and hopefully the error will be gone.

[velocirraptor23]

It ran but it did not finish properly, so tried to restart and I got this new error.

191 2026-08-08 07:45:58.849 | INFO | somd2.runner._base:init:105 - somd2 version: 2026.2.0.dev+52.g8504cc5
2026-08-08 07:45:58.864 | INFO | somd2.runner._base:init:106 - sire version: 2026.2.0.dev+gbf18e37
2026-08-08 07:45:58.864 | INFO | somd2.runner._base:init:107 - biosimspace version: 2026.2.0.dev+21.g9f13077e
2026-08-08 07:45:58.864 | INFO | somd2.runner._base:init:111 - loch version: 2026.2.0.dev+18.g7d2b0a4
2026-08-08 07:46:04.781 | INFO | somd2.runner._base:init:335 - Converting water topology to AMBER TIP3P format.
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /gpfs/uod-scale-01/cluster/ddu/cmmartinez001/Projects/openB/test_snake/scrip │
│ ts/rbfe2/production_redesigned.py:424 in │
│ │
│ 421 │
│ 422 │
│ 423 if name == "main": │
│ ❱ 424 │ runner = main() │
│ 425 │ if runner is not None: │
│ 426 │ │ runner.run() │
│ 427 │
│ │
│ /gpfs/uod-scale-01/cluster/ddu/cmmartinez001/Projects/openB/test_snake/scrip │
│ ts/rbfe2/production_redesigned.py:418 in main │
│ │
│ 415 │ elif engine == "gromacs": │
│ 416 │ │ setup_gromacs(args, lig1, lig2, lam_arr, working_dir) │
│ 417 │ elif engine == "somd2": │
│ ❱ 418 │ │ return run_somd2(args, lam_arr, working_dir) │
│ 419 │ │
│ 420 │ return None │
│ 421 │
│ │
│ /gpfs/uod-scale-01/cluster/ddu/cmmartinez001/Projects/openB/test_snake/scrip │
│ ts/rbfe2/production_redesigned.py:396 in run_somd2 │
│ │
│ 393 │ │ raise │
│ 394 │ │
│ 395 │ if runner_type == "repex": │
│ ❱ 396 │ │ runner = RepexRunner(system, config) │
│ 397 │ │ runner.run() │
│ 398 │ │ return None │
│ 399 │
│ │
│ /cluster/ddu/cmmartinez001/miniconda3/envs/openbiosim2/lib/python3.12/site-p │
│ ackages/somd2/runner/_repex.py:1198 in init │
│ │
│ 1195 │ │ │ ) │
│ 1196 │ │ │
│ 1197 │ │ # Call the base class constructor. │
│ ❱ 1198 │ │ super().init(system, config) │
│ 1199 │ │ │
│ 1200 │ │ # Make sure we're using the CUDA or OpenCL platform. │
│ 1201 │ │ if self._config.platform not in ["cuda", "opencl"]: │
│ │
│ /cluster/ddu/cmmartinez001/miniconda3/envs/openbiosim2/lib/python3.12/site-p │
│ ackages/somd2/runner/_base.py:609 in init │
│ │
│ 606 │ │ │
│ 607 │ │ # Need to verify before doing any directory checks. │
│ 608 │ │ if self._config.restart: │
│ ❱ 609 │ │ │ self._verify_restart_config() │
│ 610 │ │ │
│ 611 │ │ # Check the output directories and create names of output fil │
│ 612 │ │ self._filenames = self._prepare_output() │
│ │
│ /cluster/ddu/cmmartinez001/miniconda3/envs/openbiosim2/lib/python3.12/site-p │
│ ackages/somd2/runner/_base.py:1974 in _verify_restart_config │
│ │
│ 1971 │ │ │ │ │ "Cannot validate restart config without a config. │
│ 1972 │ │ │ │ ) │
│ 1973 │ │ │
│ ❱ 1974 │ │ self._compare_configs(self._last_config, config) │
│ 1975 │ │
│ 1976 │ @staticmethod │
│ 1977 │ def _systems_are_same(system0, system1, num_gcmc_waters=0): │
│ │
│ /cluster/ddu/cmmartinez001/miniconda3/envs/openbiosim2/lib/python3.12/site-p │
│ ackages/somd2/runner/_base.py:1920 in _compare_configs │
│ │
│ 1917 │ │ │ │ elif key == "gcmc_frequency" and v1 is None: │
│ 1918 │ │ │ │ │ continue │
│ 1919 │ │ │ │ elif v1 != v2: │
│ ❱ 1920 │ │ │ │ │ raise ValueError( │
│ 1921 │ │ │ │ │ │ f"{key} has changed since the last run. This │
│ 1922 │ │ │ │ │ │ "allowed when using the restart option." │
│ 1923 │ │ │ │ │ ) │
╰──────────────────────────────────────────────────────────────────────────────╯
ValueError: checkpoint_frequency has changed since the last run. This is not
allowed when using the restart option.

Cesar

[lohedges]

Have you changed the checkpoint_frequency for the restart? If so, this is restricted.