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Currently the repo contains the standard name `turbulent_kinetic_energy` with units of `J`. However, in atmospheric science the default units for TKE is `J kg-1`, which are the units for the variable…
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@ethrane and @kauchettl propose this as a key question. This question would cover topics like tidal disruption events, black holes + neutron stars, gravitational waves, supernovae, fast radio bursts i…
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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.
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Collecting pymbar
Using cached pymbar-2.1.0-beta.tar.gz
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I noticed that some people (for example: https://github.com/MobleyLab/alchemical-analysis/blob/37b21ebb6d0495990c43595d9ade10c779c3ab08/alchemical_analysis/alchemical_analysis.py#L650) just use the su…
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See below images from the second half of this notebook: https://github.com/choderalab/assaytools/blob/master/data/spectra/Spectra-Analysis.ipynb
Hoping this will clear up with increased sampling...
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I wanted to restart the discussion about how we should best implement constant-pH methods into OpenMM, and most importantly, which layer this should be implemented into.
The best strategy is to combi…
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Trying to enumerate all the ways that perses can be used, and might be used in future
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![image](https://github.com/user-attachments/assets/695ae124-a7eb-4c97-9ede-cffc4557b78f)
Recent changes appear to have broken the matplotlib heatmaps. @DanielYang59
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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…