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`depsy` is misclassifying [pymbar](https://github.com/choderalab/pymbar), a scientific code for analyzing data from multiple equilibrium simulations, as "Not research software".
http://depsy.org/pack…
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Pymbar is making JAX optional with pymbar-core (no JAX) and pymbar (with JAX)
https://github.com/choderalab/pymbar/issues/500
Do we want to have a similar arrangement of alchemlyb-core and alcheml…
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Hi,
I am getting the following error while running poltype.py. Could you please help me to fix the issue. Also it is using psi4 how can use gaussian instead.
```
/storage/nas_scr/shared/groups/va…
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```
from alchemtest.gmx import load_ABFE
from alchemlyb.parsing.gmx import extract_u_nk
import pandas as pd
import pymbar
df = pd.concat([extract_u_nk(data, 310) for data in load_ABFE()['data']…
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I've noticed that for some systems legs fail due to:
```
ParameterError: Warning: Should have \sum_n W_nk = 1. Actual column sum for state 0 was 0.990260. 15 other columns have similar problems
``…
tlhr updated
4 months ago
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In multistatesamplersanalyzer, the return of `_get_equilibration_data` can sometimes include a non integer `n_uncorrelated_iterations`.
In practice you wouldn't operate on fraction of an iteration,…
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I get the following error messages. Seems to just be an issue with compiling the helper code, so will go away with 3.0.
---
Collecting pymbar
Using cached pymbar-2.1.0-beta.tar.gz
…
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`pymbar` 3.0 is going to be a bit of a mess due to untested code, occasionally unstable solvers, and lack of unified documentation. Fixing many of these things will require API changes, so we want to …
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We should add functionality to perses to estimate the overlap matrix between the states. Perhaps a plot + data serialized to text would be the best?
https://pymbar.readthedocs.io/en/master/mbar.htm…
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I think there is a bug with `Simulation.sample_history()` here:
https://github.com/choderalab/perses/blob/f3aacde3588e5b90e67a21052d914a033d3c087b/perses/analysis/load_simulations.py#L235
If you'v…