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The dE method in decorrelating the u_nk data is not actually dE #299

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xiki-tempula opened this issue Mar 18, 2023 · 2 comments · Fixed by #300
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The dE method in decorrelating the u_nk data is not actually dE #299

xiki-tempula opened this issue Mar 18, 2023 · 2 comments · Fixed by #300
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@xiki-tempula
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xiki-tempula commented Mar 18, 2023 •
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Fro Gromacs each column in the u_nk is the dE between the reduced potential of the current lambda (the lambda of the column) and the reduced potential of the lambda that is being simulated. So for the dE method in decorrelation, we just use the column after or before the current lambda as it is already dE.

However, this assumption is not always the case particularly when one wants to use the function to decorrelate the openmmtools output where one could just put in a dataframe where each column is the reduced potential of that lambda window. In this case, the decorrelation will be based on the reduced potential instead of dE.
@xiki-tempula xiki-tempula self-assigned this Mar 18, 2023
@xiki-tempula xiki-tempula mentioned this issue Mar 18, 2023
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@xiki-tempula xiki-tempula linked a pull request Mar 18, 2023 that will close this issue
Fix the dE method for AMBER #300
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It seems that this is an issue for amber as well.

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orbeckst commented Mar 20, 2023 •
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Note for anyone looking at this issue to understand how PR #300 changed the behavior (in particular for GROMACS), see #300 (comment)

orbeckst pushed a commit that referenced this issue Mar 21, 2023
@xiki-tempula
Fix the dE method for AMBER (#300)
2c1d153 
* fix #299 
* Fix the dE method in u_nk2series to use the difference between two
   lambda columns instead of using the next lambda column or the previous
   column for the last window 
* change tests (GROMACS results changed)
* Update CHANGES
@orbeckst orbeckst added this to the 2.0.1 milestone Apr 5, 2023
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Fix the dE method for AMBER alchemistry/alchemlyb
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