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The ReactionPlugins could be used for analysis of existing MD runs. We could implement loading of trajectories in two ways
* Make KIMMDY work without running MD. This means, KIMMDY should load Traj…
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`> assert all(np.isclose(k_array, k_ref))`
https://github.com/hits-mbm-dev/kimmdy/actions/runs/5831559782/job/15815211115
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Currently the large integration test `test_integration_whole_run` fails
```
/hits/fast/mbm/buhrjk/phd/kimmdy/test_changemanager/src/kimmdy/changemanager.py:612: in compare_
ff_impropers
improp…
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I think the __str__ method of Topology is problematic for our logging. Is it necessary somewhere? If not, I would just remove it because the __repr__ seems fine for me.
https://github.com/hits-mbm-…
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last currently failing tests: https://github.com/hits-mbm-dev/kimmdy/actions/runs/6124770767/job/16625392110#step:4:4179
```
ERROR plugins/default_reactions/test_default_reactions.py::test_fail_lo…
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```
01-08-2023 13:21: INFO: Welcome to KIMMDY
01-08-2023 13:21: INFO: KIMMDY is running with these command line options:
01-08-2023 13:21: INFO: Namespace(input='kimmdy.yml', loglevel='DEBUG', logf…
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Example Hexala: Kimmdy wants to break same bond over and over again
Since after the first break the 'bond' is really stressed, rates are through the roof afterwards
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Ideally we would want people be able to install not just kimmdy but also the bundled reaction plugins, e.g. with
```bash
pip install git+https://github.com/hits-mbm-dev/kimmdy.git#egg=kimmdy[plugi…
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we should name our logger and not use the base logger as setting ours to debug sets all other base debuggers of, say, matplotlib also to debug and the console output becomes unusable
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looks like getting the gromacs data dir
https://github.com/hits-mbm-dev/kimmdy/blob/7352700f4928d3b26c0de406f56135002cd19066/src/kimmdy/utils.py#L9-L19
is not working in the docker container for the…