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Examine source of large error bars in 0.10.0 release #1041

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jchodera opened this issue Jun 13, 2022 · 4 comments · Fixed by #1050
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Examine source of large error bars in 0.10.0 release #1041

jchodera opened this issue Jun 13, 2022 · 4 comments · Fixed by #1050
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@jchodera
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The benchmark data for 0.10.0 has a few compounds with very large error bars.

image

We should take a look at these and see if there is something weird with the atom mappings, or other discernible issue.

@zhang-ivy
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zhang-ivy commented Jun 14, 2022

I've gone through the release notes and tried to pick out potential reasons why the error has increased for some mutations:

Nonte of these seem like they would be causing the increase in error bars though...

@ijpulidos
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I run the benchmark simulations without the endstates generation (unsampled_endstates: False on the template yaml) and I don't see the large error bars. So, I guess it is related to the unsampled endstates generation and likely introduced in #1023.

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@zhang-ivy
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Ah great find! Could you point me to the code you're using to compute the free energies (and errors) for the above plots?

And also could you retrieve the .nc files for one transformation (both phases, with and without unsampled endstates)? We may need take a closer look at how the free energies (and errors) are computed.

@zhang-ivy
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LInk to the code used for computing free energies: https://github.com/choderalab/perses/blob/main/perses/analysis/load_simulations.py

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3 participants