search

alchemistry / alchemlyb

the simple alchemistry library
https://alchemlyb.readthedocs.io
BSD 3-Clause "New" or "Revised" License
189 stars 49 forks source link

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

Closed xiki-tempula closed 1 year ago

xiki-tempula commented 1 year ago

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 commented 1 year ago

It seems that this is an issue for amber as well.

orbeckst commented 1 year ago

Note for anyone looking at this issue to understand how PR #300 changed the behavior (in particular for GROMACS), see https://github.com/alchemistry/alchemlyb/pull/300#issuecomment-1476630207