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I run into an error while trying to load a JAX NN model, and it took me a while to realize the problem was caused by `import pymbar`. [Here](https://github.com/choderalab/pymbar/blob/master/pymbar/mba…
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Hello,
I'm trying to extract the free energy from a number of yank experiments and some of them are throwing this error
```
WARNING: Did not converge to within specified tolerance.
max_delta …
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For certain types of overlapping distributions, the uncertainty estimate returned by BAR can be`nan`
``` python
%matplotlib inline
import numpy as np
import pymbar
from matplotlib import pyplot…
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It would be good to make the timeseries module something independent, which is installed automatically by a conda install. timeseries would be better as a standalone.
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A manuscript describing the automatic equilibration detection procedure is now available:
http://dx.doi.org/10.1101/021659
We should cite this in the code and `README.md`.
I have written a separate …
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Dear All
I am performing binding free energy of ligand with protein. While reaching at step 1918 of 2000 I am getting a NAN error as below:-
2021-03-27 07:41:57,769: ********************************…
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I have been trying to implement MBAR using the mbar python module for my analysis.
I have 10 equilibrium states (0 to 9). I am trying to get the expectation of an observable (A) in state 0 utilisi…
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I've added `timeseries.detectEquilibration()` to allow robust, automated determination of the equilibrated portion of a dataset. We should update the examples to use this.
Here's an example of usage…
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Hi there, I noticed that alchemical analysis only uses a single core at a time and doesn't utilize gpus at all. I'm wondering if their is any intent of adding this to the code in the near future?
Gene…
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I have alreadly applied `pymbar` to umbrella sampling data successfully. Now I'd like to compute the effective mass of CV at the transition state. A function `compute_expectations` under `MBAR` can g…