Bugfix LJ Correction #425
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Bugfix LJ Correction #425
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…and that all molecules are searched (first and last molecules could both be non-solvent) [ci skip]
… averaging [ci skip]
…esting of LJ correction [ci skip]
chryswoods
added a commit
to OpenBioSim/sire
that referenced
this pull request
Jan 17, 2023
) and [michellab/Sire/pull/425](michellab/Sire#425). Thanks to [@fjclark](https://github.com/fjclark) for submitting. Sorry for the lack of authorship - I had to copy these files in manually across to the openbiosim repo.
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Hi @fjclark - Just to let you know that I have now merged this all into openbiosim/sire and it has been released as version If it is ok, I will close this pull request (and the other request) as these are now merged into the openbiosim code. |
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Hi @chryswoods, thanks very much. Of course. |
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This PR fixes the LJ correction and closes this issue.
I found two issues with the script:
1 . The LJ correction script consistently worked for me with Sire 2021.1.0, but started to fail for the complex legs of ABFE calculations for Sire 2022.1.0. This was due to overflow in the calculation of the exponential average of free energies. For energies more positive than - 420 kcal per mol at 298 K, exp(-E/kT) was just less than 1.7E308, causing no issues. However, for the complex, the LJ energy was greater, causing overflow of the float64s. The smaller LJ energy with the solvent leg system meant there were no issues. I'm not sure what update made for Sire 2022.1.0 caused the LJ energy of my complex leg system to increase to the extent that this issue surfaced. I've fixed this by subtracting the mean of the energies before exponential averaging and adding back on afterwards.
I've made the script compatible with recent changes to OpenMMMD.py. I've also modified runLambda() to return the correction, and resolveParameters() to allow return values to allow me to write a test for the correction. I'll open a PR for the test shortly.