Conformational entropy differences between versions

[ioanaapapa]

I'm a bit unsure if maybe the bug isn't just in the previous version of the code and the new values are fine but I wanted to check?
Results for the united atom conformational entropy obtained using the two versions are quite different, with new total conformational entropy being about 400 J/mol K higher.

Trends per residue are consistent, with aliphatic residues generally having higher entropies with the newer code and bulky aromatic residues having much higher entropies with the old code (I would expect those to have low conformational entropies as the aromatic rings are rigid and also big and probably will hinder rotations around bonds and make less conformations accessible.) I've attached a plot showing the differences between values per residue with each code.

Both codes should be looking at SC dihedrals only. Both give 0 for glycine, which does not have any SC dihedrals, as expected.

[skfegan]

Which of the topological methods were you using for the 0.3.6 version as that code had several options?

[ioanaapapa]

The adaptive method, the one that has the "--topog 3" flag and should be similar to the one adapted in the new implementation.

[ioanaapapa]

Can I help with testing and analysing this? I'd be happy to do so.

[jimboid]

Can I help with testing and analysing this? I'd be happy to do so.

Please do, assign yourself to this issue so we can keep track of who is looking at what. Keep us updated on your progress. There are some variation in the implementation of the two versions, the new code has additional parts of theory implemented..