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Perhaps I should reopen an issue and describe it [here](https://github.com/Gallicchio-Lab/AToM-OpenMM/issues/21#issuecomment-2212364700).
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Given the high impact of updateParametersInContext() code on the performance of FEP calculations with SOMD2 (benchmark https://github.com/openmm/openmm/pull/4610) it would be a very useful feature to …
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We're seeing convergence issues on very innocuous transformations when using PyMBAR 4, e.g. lig_ejm_31 to lig_ejm_50 from the tyk2 set.
We'll need to dig into it and work out why this is happening.…
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I saw that there was a patch made in July to pin to pymbar 3 (https://github.com/choderalab/yank/pull/1285) - Are there plans to also support pymbar 4?
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Are there plans to update this to work with the new pymbar? Is this something that I could help out with?
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I have a use case where I need some components of the pymbar that is not solver related like the decorrelation, so I install `pymbar-core=4`. In the same environment, I install openfe, which then pull…
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The new release of [pymbar](https://github.com/choderalab/pymbar/releases/tag/4.0.1) has some API changes which have broken the imports in Forcebalance. Maybe it would be good to add a nightly CI test…
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Hi,
I am using pymbar through David Mobley's alchemical-analysis tool. I
want to do BAR/MBAR analysis with AMBER. Strangely, AMBER will
occasionally output very high energies, sometimes not even di…
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Hello.
I am trying to run some Temperature replica exchange simulations for small molecules. The relevant part of my script is as follows.
```
# Set up the temperature range for replicas
n_replica…
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Just a note regarding the release of `pymbar 4.0`, which has breaking API changes, as documented [here](https://pymbar.readthedocs.io/en/master/moving_from_pymbar3.html). We'll likely need to update t…