openmmtools

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add python 3.10 to CI

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## Description Provide a brief description of the PR's purpose here. ## Todos - [ ] Implement feature / fix bug - [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests) - [ ] Update...

mikemhenry

Deserializing nc file generated with openmmtools < 0.21.5 yields key error when loading with openmmtools 0.21.5 because of missing constraint tolerance

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```python from openmmtools.multistate import MultiStateReporter main_dir = 45 replicate = 0 sub_dir = 3 phase = 'complex' path = f"/data/chodera/zhangi/perses_benchmark/repex/perses-bnbs-paper-first-attempt/{main_dir}/{sub_dir}/replicate_{replicate}/perses-paper2/{sub_dir}/{sub_dir}_{phase}.nc" reporter = MultiStateReporter(path, open_mode='r') reporter.read_mcmc_moves() ``` ``` --------------------------------------------------------------------------- KeyError Traceback...

zhang-ivy

extend on resume

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## Description This PR allows the number of timesteps to be increased upon resuming a simulation. See https://github.com/choderalab/yank/pull/1283 ## Todos - [ ] Implement feature / fix bug - [...

jfennick

Avoid raising broad `Exception` when raising errors

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Some check and errors are raised with generic `Exception` objects, this can lead to some troubles in the future even if we are safe now. We should enhance our code...

ijpulidos

`openmm-ml` compatibility for generic `MultiStateSampler` objects

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## Description implement compatibility for [openmm-ml](https://github.com/openmm/openmm-ml) (and openmm 8/beta) to allow for generic `MultiStateSampler` free energy/sampling calculations. ## Todos - [ ] Implement feature / fix bug - [ ]...

dominicrufa

Add support for receptor dimers

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## Description Provide a brief description of the PR's purpose here. I'm performing a simulation using Yank of a system in which the receptor is a dimer. This causes the...

jfennick

We want to port the notebook analysis and analyzer objects to `openmmtools`. CC https://github.com/choderalab/yank/issues/1282

ijpulidos

Resuming and basic tests with MPI context

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While working on #602 it was noted that the issue is only relevant when the simulations are run using 2 or more MPI processes (multiple GPUs). Therefore, we need a...

ijpulidos

Positions not updating during PT simulation

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Hello I am attempting to run some PT simulations, but there is something kind of funky going on. Whenever I set up the simulation and run the positions do not...

clarktemple03

Renaming (or aliasing?) `online_analysis_interval`

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Note that we may also want to consider opening an issue for renaming `self.online_analysis_interval` to `self.offline_analysis_interval` _Originally posted by @zhang-ivy in https://github.com/choderalab/openmmtools/issues/592#issuecomment-1149053115_

ijpulidos