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Conformational Entropy Changes #235
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Thanks for reporting @ioanaapapa.
What would really helpful, because there are 3 changes that might have caused this, is either can you drop your parameters for how you ran this example to allow us to reproduce for 1.0.3 and then run some tests against the other versions. Or you could create separate conda envs with 1.0.4, 1.0.5 and see which version the issue start with which would tell us which of the changes brought about the difference.
These are the log files for when I ran this with 1.0.3:
And these are the topology and trajectory for just the ligand:
Thanks. Will have a look
I’ve now had the opportunity to run four versions of CodeEntropy using identical inputs, driven by the same
config.yamlfile.--- run1: top_traj_file: ["../../test_data/G1_traj/G1_stripped.tpr", "../../test_data/G1_traj/G1_stripped.trr"] selection_string: 'resname LIG' temperature: 300
From an initial comparison, the first noticeable difference appears between
v1.0.3andv1.0.4. Specifically, the conformational entropy for group 0 at the united‑atom level changes from:21.338046088170707inv1.0.3- to
49.94564885738359inv1.0.4
The latter value is then unchanged in subsequent releases.
CodeEntropy version Conformational entropy v1.0.321.338046088170707 v1.0.449.94564885738359 v1.0.549.94564885738359 v1.0.649.94564885738359 The change is introduced in
v1.0.4, which corresponds to thev1.0.4release tag. One potential explanation for this behaviour may be changes introduced in PR #167, which appears to be the most relevant modification in that release that could affect conformational entropy calculations.I've also attached all of the final results for each version if you would like to look into those with more detail.
v1.0.3-output_file.json
v1.0.4-output_file.json
v1.0.5-output_file.json
v1.0.6-output_file.jsonIt looks like the conformational entropy doesn't change with the number of frames.
Closed by PR #267.
Reacted by Harry Swift- linked a pull request that will close this issueAlign CodeEntropy with entropy methods used in 2019 paper #267
on Feb 5, 2026
Conformational entropy results for the small molecules are now significantly higher - seem unusually high and no longer match the SAMPL paper ones. The difference happened sometime after CodeEntropy1.0.3 and before the conformational entropy averaging PR, which did not affect this issue.
For G1, one of the guest molecules